diff options
| author |   Repository QA checks <repo-qa-checks@gentoo.org> | 2016-04-14 08:03:00 +0000 |
|---|---|---|
| committer | Repository QA checks <repo-qa-checks@gentoo.org> | 2016-04-14 08:03:00 +0000 |
| commit | ef72a7782fe626b3ae644fe88a6f834060f93bb6 (patch) | |
| tree | e1e7be9eeababd365163248e6fa1c2df187accac /metadata/md5-cache/sci-biology | |
| parent | Add 'metadata/news/' from commit 'a526289811b6d27f57e7599684c4ce1c5631044f' (diff) | |
| download | gentoo-ef72a7782fe626b3ae644fe88a6f834060f93bb6.tar.gz gentoo-ef72a7782fe626b3ae644fe88a6f834060f93bb6.tar.bz2 gentoo-ef72a7782fe626b3ae644fe88a6f834060f93bb6.zip | |
2016-04-14 08:02:40 UTC
Diffstat (limited to 'metadata/md5-cache/sci-biology')
248 files changed, 3200 insertions, 0 deletions
diff --git a/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 b/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 new file mode 100644 index 000000000000..4bd539b5a7ed --- /dev/null +++ b/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install +DEPEND=app-arch/unzip +DESCRIPTION=A Plasmid Editor +EAPI=5 +HOMEPAGE=http://www.biology.utah.edu/jorgensen/wayned/ape/ +KEYWORDS=~amd64 ~x86 +LICENSE=ApE +RDEPEND=dev-lang/tcl:0 dev-lang/tk:0 +RESTRICT=mirror +SLOT=0 +SRC_URI=http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ApE-2.0.7.zip +_eclass_exported_funcs=src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=9632d8d4bd171156ad6edf821009dbc6 diff --git a/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 b/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 new file mode 100644 index 000000000000..0ec9212f8acf --- /dev/null +++ b/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install postinst prepare prerm setup test unpack +DEPEND=dev-perl/Module-Build dev-perl/Capture-Tiny !<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 +DESCRIPTION=Generic Model Organism Database Project - The Generic Genome Browser +EAPI=5 +HOMEPAGE=http://gmod.org/wiki/GBrowse +IUSE=-minimal mysql postgres +sqlite vhosts +KEYWORDS=~amd64 ~x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=!<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 +SLOT=0 +SRC_URI=mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.48.tar.gz +_eclass_exported_funcs=pkg_prerm:webapp pkg_postinst:webapp pkg_setup:webapp src_unpack:perl-module src_prepare:perl-module src_configure:- src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be webapp 42c6ef7af496b228f9854b3c81e4b226 +_md5_=caf58a720664c095c77fe9b64b311dbe diff --git a/metadata/md5-cache/sci-biology/aaindex-9.1 b/metadata/md5-cache/sci-biology/aaindex-9.1 new file mode 100644 index 000000000000..a666d0ee10e3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/aaindex-9.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=Amino acid indices and similarity matrices +EAPI=0 +HOMEPAGE=http://www.genome.ad.jp/aaindex +IUSE=emboss minimal +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/aaindex-9.1.tar.bz2 +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=24c7fa19ef1b5a56372be50a08ad31e8 diff --git a/metadata/md5-cache/sci-biology/abyss-1.3.3 b/metadata/md5-cache/sci-biology/abyss-1.3.3 new file mode 100644 index 000000000000..74b8eda59ae7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/abyss-1.3.3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare +DEPEND=dev-cpp/sparsehash mpi? ( virtual/mpi ) !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +EAPI=4 +HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ +IUSE=+mpi openmp +KEYWORDS=amd64 x86 +LICENSE=abyss +RDEPEND=dev-cpp/sparsehash mpi? ( virtual/mpi ) +SLOT=0 +SRC_URI=http://www.bcgsc.ca/downloads/abyss/abyss-1.3.3.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=0cf454bdff2b93fbf261fabc9acab1dd diff --git a/metadata/md5-cache/sci-biology/abyss-1.3.6-r1 b/metadata/md5-cache/sci-biology/abyss-1.3.6-r1 new file mode 100644 index 000000000000..b839ebb5ed56 --- /dev/null +++ b/metadata/md5-cache/sci-biology/abyss-1.3.6-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare +DEPEND=dev-cpp/sparsehash dev-libs/boost misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( virtual/mpi ) misc-haskell? ( dev-lang/ghc dev-haskell/mmap ) !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +EAPI=6 +HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ +IUSE=+mpi openmp misc-haskell +KEYWORDS=~amd64 ~x86 +LICENSE=abyss +RDEPEND=dev-cpp/sparsehash dev-libs/boost misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( virtual/mpi ) +SLOT=0 +SRC_URI=http://www.bcgsc.ca/downloads/abyss/abyss-1.3.6.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=5edcc89dbe8b21d260f6545673c709d5 diff --git a/metadata/md5-cache/sci-biology/allpathslg-42337 b/metadata/md5-cache/sci-biology/allpathslg-42337 new file mode 100644 index 000000000000..b912ffad7a96 --- /dev/null +++ b/metadata/md5-cache/sci-biology/allpathslg-42337 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DEPEND=dev-libs/boost !sci-biology/allpaths sci-biology/vaal !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=De novo assembly of whole-genome shotgun microreads +EAPI=4 +HOMEPAGE=http://www.broadinstitute.org/science/programs/genome-biology/crd +KEYWORDS=amd64 -x86 +LICENSE=MIT +SLOT=0 +SRC_URI=ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-42337.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=5dbc3e63efe609db145c569cdcba1922 diff --git a/metadata/md5-cache/sci-biology/allpathslg-52488-r1 b/metadata/md5-cache/sci-biology/allpathslg-52488-r1 new file mode 100644 index 000000000000..79701b1190a0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/allpathslg-52488-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare pretend +DEPEND=!sci-biology/allpaths !sci-biology/vaal dev-libs/boost !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=De novo assembly of whole-genome shotgun microreads +EAPI=6 +HOMEPAGE=http://www.broadinstitute.org/science/programs/genome-biology/crd +IUSE=openmp +KEYWORDS=~amd64 +LICENSE=MIT +RDEPEND=!sci-biology/allpaths !sci-biology/vaal +SLOT=0 +SRC_URI=ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-52488.tar.gz +_eclass_exported_funcs=pkg_pretend:- src_prepare:- src_configure:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6161883eb3e0d1523a6d0d6889d91ce4 diff --git a/metadata/md5-cache/sci-biology/amap-2.2-r2 b/metadata/md5-cache/sci-biology/amap-2.2-r2 new file mode 100644 index 000000000000..e18fd9889fd6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/amap-2.2-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=java? ( >=virtual/jdk-1.5 ) java? ( >=dev-java/java-config-2.2.0 ) java? ( >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 ) +DESCRIPTION=Protein multiple-alignment-based sequence annealing +EAPI=2 +HOMEPAGE=http://bio.math.berkeley.edu/amap/ +IUSE=java elibc_FreeBSD java elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=java? ( >=virtual/jre-1.5 ) java? ( >=dev-java/java-config-2.2.0 ) +SLOT=0 +SRC_URI=http://baboon.math.berkeley.edu/amap/download/amap.2.2.tar.gz +_eclass_exported_funcs=pkg_preinst:java-pkg-opt-2 pkg_setup:java-pkg-opt-2 src_prepare:- src_configure:java-ant-2 src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-opt-2 40db73f27fc6458ec2105812a4f261c7 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=8010150e6242df5d294ab35b887af2a1 diff --git a/metadata/md5-cache/sci-biology/amos-3.1.0 b/metadata/md5-cache/sci-biology/amos-3.1.0 new file mode 100644 index 000000000000..ab4ca35c8d8e --- /dev/null +++ b/metadata/md5-cache/sci-biology/amos-3.1.0 @@ -0,0 +1,14 @@ +DEFINED_PHASES=prepare +DEPEND=qt4? ( dev-qt/qtcore:4 ) +DESCRIPTION=A Modular, Open-Source whole genome assembler +EAPI=4 +HOMEPAGE=http://amos.sourceforge.net/ +IUSE=qt4 +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=qt4? ( dev-qt/qtcore:4 ) dev-perl/DBI dev-perl/Statistics-Descriptive sci-biology/mummer +SLOT=0 +SRC_URI=mirror://sourceforge/amos/amos-3.1.0.tar.gz +_eclass_exported_funcs=src_prepare:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=57af6bf2b801ff256544c1ae4d6e2239 diff --git a/metadata/md5-cache/sci-biology/amos-3.1.0-r1 b/metadata/md5-cache/sci-biology/amos-3.1.0-r1 new file mode 100644 index 000000000000..8ec08466815b --- /dev/null +++ b/metadata/md5-cache/sci-biology/amos-3.1.0-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=install prepare +DEPEND=qt4? ( dev-qt/qtcore:4 ) +DESCRIPTION=A Modular, Open-Source whole genome assembler +EAPI=5 +HOMEPAGE=http://amos.sourceforge.net/ +IUSE=qt4 python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=qt4? ( dev-qt/qtcore:4 ) dev-perl/DBI dev-perl/Statistics-Descriptive sci-biology/mummer +SLOT=0 +SRC_URI=mirror://sourceforge/amos/amos-3.1.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=c6ea5f3288847da2901f769d10d3429b diff --git a/metadata/md5-cache/sci-biology/arb-5.1-r1 b/metadata/md5-cache/sci-biology/arb-5.1-r1 new file mode 100644 index 000000000000..f7212f2e4a68 --- /dev/null +++ b/metadata/md5-cache/sci-biology/arb-5.1-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare unpack +DEPEND=app-text/sablotron media-libs/libpng media-libs/tiff www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) +DESCRIPTION=Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis +EAPI=2 +HOMEPAGE=http://www.arb-home.de/ +IUSE=+opengl +KEYWORDS=~amd64 ~x86 +LICENSE=arb +RDEPEND=app-text/sablotron media-libs/libpng media-libs/tiff www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sci-visualization/gnuplot +SLOT=0 +SRC_URI=http://download.arb-home.de/release/arb_5.1/arbsrc.tgz -> arb-5.1.tgz mirror://gentoo/arb-5.1-glibc2.10.patch.bz2 https://dev.gentoo.org/~jlec/arb-5.1-linker.patch.bz2 +_eclass_exported_funcs=src_unpack:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=ccac55e99a86ba7bca4258e0de6a277a diff --git a/metadata/md5-cache/sci-biology/arb-5.2 b/metadata/md5-cache/sci-biology/arb-5.2 new file mode 100644 index 000000000000..468488a5d5c0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/arb-5.2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare unpack +DEPEND=app-text/sablotron media-libs/libpng media-libs/tiff www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sys-process/time +DESCRIPTION=Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis +EAPI=4 +HOMEPAGE=http://www.arb-home.de/ +IUSE=+opengl +KEYWORDS=~amd64 ~x86 +LICENSE=arb +RDEPEND=app-text/sablotron media-libs/libpng media-libs/tiff www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sci-visualization/gnuplot +SLOT=0 +SRC_URI=http://download.arb-home.de/release/arb_5.2/arbsrc.tgz -> arb-5.2.tgz https://dev.gentoo.org/~jlec/distfiles/arb-5.2-linker.patch.bz2 +_eclass_exported_funcs=src_unpack:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=c1e75a5c097ccea22adb427050d7ea9a diff --git a/metadata/md5-cache/sci-biology/arb-5.3 b/metadata/md5-cache/sci-biology/arb-5.3 new file mode 100644 index 000000000000..d462d8cca688 --- /dev/null +++ b/metadata/md5-cache/sci-biology/arb-5.3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare unpack +DEPEND=app-text/sablotron media-libs/libpng media-libs/tiff www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sys-process/time +DESCRIPTION=Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis +EAPI=4 +HOMEPAGE=http://www.arb-home.de/ +IUSE=+opengl +KEYWORDS=~amd64 ~x86 +LICENSE=arb +RDEPEND=app-text/sablotron media-libs/libpng media-libs/tiff www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sci-visualization/gnuplot +SLOT=0 +SRC_URI=http://download.arb-home.de/release/arb_5.3/arbsrc.tgz -> arb-5.3.tgz https://dev.gentoo.org/~jlec/distfiles/arb-5.3-linker.patch.xz +_eclass_exported_funcs=src_unpack:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6f4ceede9236fd4baf2032128fab2349 diff --git a/metadata/md5-cache/sci-biology/ariadne-1.3-r1 b/metadata/md5-cache/sci-biology/ariadne-1.3-r1 new file mode 100644 index 000000000000..90dcc41ed864 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ariadne-1.3-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install unpack +DEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 +DESCRIPTION=Protein sequences and profiles comparison +EAPI=0 +HOMEPAGE=http://www.well.ox.ac.uk/ariadne/ +KEYWORDS=~amd64 x86 +LICENSE=ARIADNE +RDEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 +SLOT=0 +SRC_URI=http://www.well.ox.ac.uk/ariadne/ariadne-1.3.tar.Z +_eclass_exported_funcs=src_unpack:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=1742c4b03c22637909dd5c35478feffe diff --git a/metadata/md5-cache/sci-biology/ariadne-1.3-r2 b/metadata/md5-cache/sci-biology/ariadne-1.3-r2 new file mode 100644 index 000000000000..c25e704a09ec --- /dev/null +++ b/metadata/md5-cache/sci-biology/ariadne-1.3-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare +DEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 +DESCRIPTION=Protein sequences and profiles comparison +EAPI=4 +HOMEPAGE=http://www.well.ox.ac.uk/ariadne/ +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=ARIADNE +RDEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 +SLOT=0 +SRC_URI=http://www.well.ox.ac.uk/ariadne/ariadne-1.3.tar.Z +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6760dd272f3876553a07c32a95d4f672 diff --git a/metadata/md5-cache/sci-biology/augustus-2.5.5 b/metadata/md5-cache/sci-biology/augustus-2.5.5 new file mode 100644 index 000000000000..c63257e8e329 --- /dev/null +++ b/metadata/md5-cache/sci-biology/augustus-2.5.5 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Eukaryotic gene predictor +EAPI=4 +HOMEPAGE=http://augustus.gobics.de/ +IUSE=examples +KEYWORDS=amd64 x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=d0f9ba272acefc27ec7b12c6d3b2b01d diff --git a/metadata/md5-cache/sci-biology/bamtools-1.0.2-r1 b/metadata/md5-cache/sci-biology/bamtools-1.0.2-r1 new file mode 100644 index 000000000000..c364296d07f5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-1.0.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-libs/jsoncpp sys-libs/zlib sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=5 +HOMEPAGE=https://github.com/pezmaster31/bamtools +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=dev-libs/jsoncpp sys-libs/zlib +SLOT=0 +SRC_URI=mirror://github/pezmaster31/bamtools/bamtools-1.0.2.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:cmake-utils src_compile:cmake-utils src_test:cmake-utils src_install:- +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=7510135c49b6f635124664572ea56bb2 diff --git a/metadata/md5-cache/sci-biology/bamtools-2.3.0 b/metadata/md5-cache/sci-biology/bamtools-2.3.0 new file mode 100644 index 000000000000..af43de045936 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-2.3.0 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=dev-libs/jsoncpp-0.5.0-r1 <dev-libs/jsoncpp-1 sys-libs/zlib sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=5 +HOMEPAGE=https://github.com/pezmaster31/bamtools +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=>=dev-libs/jsoncpp-0.5.0-r1 <dev-libs/jsoncpp-1 sys-libs/zlib +SLOT=0 +SRC_URI=https://github.com/pezmaster31/bamtools/archive/v2.3.0.tar.gz -> bamtools-2.3.0.tar.gz +_eclass_exported_funcs=src_prepare:cmake-utils src_configure:cmake-utils src_compile:cmake-utils src_test:cmake-utils src_install:- +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=14b6521e2975f38128d76c7ba4a5fb31 diff --git a/metadata/md5-cache/sci-biology/beast-mcmc-1.7.5-r1 b/metadata/md5-cache/sci-biology/beast-mcmc-1.7.5-r1 new file mode 100644 index 000000000000..eea5b49137c5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/beast-mcmc-1.7.5-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install preinst prepare setup test +DEPEND=>=virtual/jdk-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0 >=dev-java/ant-core-1.8.2:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences +EAPI=5 +HOMEPAGE=https://github.com/beast-dev/beast-mcmc +IUSE=elibc_FreeBSD elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=LGPL-3 +RDEPEND=>=virtual/jre-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0 +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/beast-mcmc-1.7.5.tar.xz +_eclass_exported_funcs=pkg_preinst:java-pkg-2 pkg_setup:java-pkg-2 src_prepare:- src_configure:java-ant-2 src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-2 b02dc1e46b3648e467b5fbdf7857cf28 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=78a597e327e0b56f4074f590ef3eca4c diff --git a/metadata/md5-cache/sci-biology/beast-mcmc-9999 b/metadata/md5-cache/sci-biology/beast-mcmc-9999 new file mode 100644 index 000000000000..b4592b4b8260 --- /dev/null +++ b/metadata/md5-cache/sci-biology/beast-mcmc-9999 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install preinst prepare setup test unpack +DEPEND=>=virtual/jdk-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0 >=dev-java/ant-core-1.8.2:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2 || ( dev-vcs/subversion[http] dev-vcs/subversion[webdav-neon] dev-vcs/subversion[webdav-serf] ) net-misc/rsync +DESCRIPTION=Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences +EAPI=2 +HOMEPAGE=https://github.com/beast-dev/beast-mcmc +IUSE=elibc_FreeBSD elibc_FreeBSD +LICENSE=LGPL-3 +RDEPEND=>=virtual/jre-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0 +SLOT=0 +_eclass_exported_funcs=pkg_preinst:subversion pkg_setup:java-pkg-2 src_unpack:subversion src_prepare:- src_configure:java-ant-2 src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-2 b02dc1e46b3648e467b5fbdf7857cf28 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 subversion 4fee0a764150bb4dda27ed4d2c4ed7ce toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=91fd25b95c1888b46de27b583565e9d0 diff --git a/metadata/md5-cache/sci-biology/bedtools-2.16.2 b/metadata/md5-cache/sci-biology/bedtools-2.16.2 new file mode 100644 index 000000000000..39266d0d47a9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bedtools-2.16.2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats +EAPI=4 +HOMEPAGE=https://github.com/arq5x/bedtools2 +KEYWORDS=~x86 ~amd64 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://bedtools.googlecode.com/files/BEDTools.v2.16.2.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=b94632a5016d667839021935025ec232 diff --git a/metadata/md5-cache/sci-biology/bedtools-2.20.1 b/metadata/md5-cache/sci-biology/bedtools-2.20.1 new file mode 100644 index 000000000000..705b7f4ee61a --- /dev/null +++ b/metadata/md5-cache/sci-biology/bedtools-2.20.1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats +EAPI=4 +HOMEPAGE=https://github.com/arq5x/bedtools2 +KEYWORDS=~x86 ~amd64 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2d2463a3300cf65fbdc35148dc17f093 diff --git a/metadata/md5-cache/sci-biology/bfast-0.7.0a b/metadata/md5-cache/sci-biology/bfast-0.7.0a new file mode 100644 index 000000000000..063c3d955351 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bfast-0.7.0a @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Blat-like Fast Accurate Search Tool +EAPI=5 +HOMEPAGE=https://sourceforge.net/projects/bfast/ +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-perl/XML-Simple +SLOT=0 +SRC_URI=mirror://sourceforge/bfast/bfast-0.7.0a.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:autotools-utils src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=78320f55e4a3ad5d498ceb56ecbc3171 diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0 b/metadata/md5-cache/sci-biology/biogrep-1.0 new file mode 100644 index 000000000000..7557775d4bed --- /dev/null +++ b/metadata/md5-cache/sci-biology/biogrep-1.0 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=Multithreading application for matching large sets of patterns against biosequence dbs. +EAPI=0 +HOMEPAGE=http://web.mit.edu/bamel/biogrep.shtml +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://web.mit.edu/bamel/biogrep-1.0.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=35e5d2f17b0523cc4607f5fc186d0453 diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0-r1 b/metadata/md5-cache/sci-biology/biogrep-1.0-r1 new file mode 100644 index 000000000000..8e55388d189b --- /dev/null +++ b/metadata/md5-cache/sci-biology/biogrep-1.0-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Multithreading application for matching large sets of patternsagainst biosequence dbs +EAPI=3 +HOMEPAGE=http://web.mit.edu/bamel/biogrep.shtml +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://web.mit.edu/bamel/biogrep-1.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=1dfeddc4aec877d95b036ca150a63ec5 diff --git a/metadata/md5-cache/sci-biology/biopandas-0.1.4 b/metadata/md5-cache/sci-biology/biopandas-0.1.4 new file mode 100644 index 000000000000..2578f8766045 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopandas-0.1.4 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] test? ( dev-python/nose[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_3? ( >=dev-lang/python-3.3.2-r2:3.3 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +DESCRIPTION=Molecular Structures in Pandas DataFrames +EAPI=5 +HOMEPAGE=https://rasbt.github.io/biopandas/ https://github.com/rasbt/biopandas https://pypi.python.org/pypi/BioPandas +IUSE=test python_targets_python2_7 python_targets_python3_3 python_targets_python3_4 python_targets_python3_5 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD +RDEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_3? ( >=dev-lang/python-3.3.2-r2:3.3 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_3 python_targets_python3_4 python_targets_python3_5 ) +SLOT=0 +SRC_URI=mirror://pypi/B/BioPandas/biopandas-0.1.4.tar.gz +_eclass_exported_funcs=src_prepare:distutils-r1 src_configure:distutils-r1 src_compile:distutils-r1 src_test:distutils-r1 src_install:distutils-r1 +_eclasses_=distutils-r1 4e8ac1ba76ddacd8f7c0289aa586a34c eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=91683944bda72d8b5f7f71f9ee5f3217 diff --git a/metadata/md5-cache/sci-biology/bioperl-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-1.6.9 new file mode 100644 index 000000000000..269e113fcb25 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-1.6.9 @@ -0,0 +1,16 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/yaml dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/set-scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Core modules +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal graphviz sqlite +db +network +run +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +PDEPEND=db? ( >=sci-biology/bioperl-db-1.6.9 ) network? ( >=sci-biology/bioperl-network-1.6.9 ) run? ( >=sci-biology/bioperl-run-1.6.9 ) +RDEPEND=dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/yaml dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/set-scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] +REQUIRED_USE=minimal? ( !graphviz ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz +_eclass_exported_funcs=src_unpack:perl-module src_prepare:perl-module src_configure:perl-module src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=caa3e2aaa47222a4fe2d6db0952a6bfa diff --git a/metadata/md5-cache/sci-biology/bioperl-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-9999-r1 new file mode 100644 index 000000000000..8959fcc9f859 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-9999-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build dev-perl/Data-Stag dev-perl/libwww-perl !minimal? ( dev-perl/Ace dev-perl/Bio-ASN1-EntrezGene dev-perl/Spreadsheet-ParseExcel dev-perl/Spreadsheet-WriteExcel >=dev-perl/XML-SAX-0.15 dev-perl/Graph dev-perl/SOAP-Lite dev-perl/Array-Compare dev-perl/SVG dev-perl/XML-Simple dev-perl/XML-Parser dev-perl/XML-Twig >=dev-perl/HTML-Parser-3.60 >=dev-perl/XML-Writer-0.4 dev-perl/Clone dev-perl/XML-DOM dev-perl/set-scalar dev-perl/XML-XPath dev-perl/XML-DOM-XPath dev-perl/Algorithm-Munkres dev-perl/Data-Stag dev-perl/Math-Random dev-perl/PostScript dev-perl/Convert-Binary-C dev-perl/SVG-Graph ) graphviz? ( dev-perl/GraphViz ) dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl tools for bioinformatics - Core modules +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal graphviz +db +network +run +LICENSE=Artistic GPL-2 +PDEPEND=!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) db? ( >=sci-biology/bioperl-db-9999 ) network? ( >=sci-biology/bioperl-network-9999 ) run? ( >=sci-biology/bioperl-run-9999 ) +RDEPEND=dev-perl/Data-Stag dev-perl/libwww-perl !minimal? ( dev-perl/Ace dev-perl/Bio-ASN1-EntrezGene dev-perl/Spreadsheet-ParseExcel dev-perl/Spreadsheet-WriteExcel >=dev-perl/XML-SAX-0.15 dev-perl/Graph dev-perl/SOAP-Lite dev-perl/Array-Compare dev-perl/SVG dev-perl/XML-Simple dev-perl/XML-Parser dev-perl/XML-Twig >=dev-perl/HTML-Parser-3.60 >=dev-perl/XML-Writer-0.4 dev-perl/Clone dev-perl/XML-DOM dev-perl/set-scalar dev-perl/XML-XPath dev-perl/XML-DOM-XPath dev-perl/Algorithm-Munkres dev-perl/Data-Stag dev-perl/Math-Random dev-perl/PostScript dev-perl/Convert-Binary-C dev-perl/SVG-Graph ) graphviz? ( dev-perl/GraphViz ) dev-lang/perl:=[-build(-)] +SLOT=0 +_eclass_exported_funcs=src_unpack:git-2 src_prepare:perl-module src_configure:- src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e git-2 672c3929a162f221a53b4ccb4d25d8a2 multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=e4c2ed3c2206bd745e94a0dd5ae9e19f diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 new file mode 100644 index 000000000000..8891468bd5a2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-perl/Module-Build dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz +_eclass_exported_funcs=src_unpack:perl-module src_prepare:perl-module src_configure:perl-module src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=c86ac1da0676ffecc4a6d1473143a1ea diff --git a/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 new file mode 100644 index 000000000000..5cf269bedc9f --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +LICENSE=Artistic GPL-2 +RDEPEND=>=sci-biology/bioperl-9999 dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] +SLOT=0 +_eclass_exported_funcs=src_unpack:git-2 src_prepare:perl-module src_configure:- src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e git-2 672c3929a162f221a53b4ccb4d25d8a2 multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=0b002dfc84485c315f3a837fdf29a6ba diff --git a/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 new file mode 100644 index 000000000000..72b077101877 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Network-1.006900.tar.gz +_eclass_exported_funcs=src_unpack:perl-module src_prepare:perl-module src_configure:perl-module src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=57636449f55fd44067e7024bcb3be832 diff --git a/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 new file mode 100644 index 000000000000..d89a3c7295dd --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +LICENSE=Artistic GPL-2 +RDEPEND=>=sci-biology/bioperl-9999 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +SLOT=0 +_eclass_exported_funcs=src_unpack:git-2 src_prepare:perl-module src_configure:perl-module src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e git-2 672c3929a162f221a53b4ccb4d25d8a2 multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=637485289bf69287c429734619a346eb diff --git a/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 new file mode 100644 index 000000000000..beb3fb348cb1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] +RESTRICT=test +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz +_eclass_exported_funcs=src_unpack:perl-module src_prepare:perl-module src_configure:perl-module src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=019ccce216c420ea65d9cf1925a8de4b diff --git a/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 new file mode 100644 index 000000000000..49f67cea4574 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run ) dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal test +LICENSE=Artistic GPL-2 +RDEPEND=>=sci-biology/bioperl-9999 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run ) dev-lang/perl:=[-build(-)] +RESTRICT=test +SLOT=0 +_eclass_exported_funcs=src_unpack:git-2 src_prepare:perl-module src_configure:perl-module src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e git-2 672c3929a162f221a53b4ccb4d25d8a2 multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=580d88609d793360e4dac4df84e90155 diff --git a/metadata/md5-cache/sci-biology/biopython-1.65 b/metadata/md5-cache/sci-biology/biopython-1.65 new file mode 100644 index 000000000000..278621378ba2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopython-1.65 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] media-gfx/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] sys-devel/flex python_targets_pypy? ( virtual/pypy:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_3? ( >=dev-lang/python-3.3.2-r2:3.3 ) python_targets_python3_4? ( dev-lang/python:3.4 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-)] +DESCRIPTION=Python modules for computational molecular biology +EAPI=5 +HOMEPAGE=http://www.biopython.org/ https://pypi.python.org/pypi/biopython/ +IUSE=python_targets_pypy python_targets_python2_7 python_targets_python3_3 python_targets_python3_4 +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux +LICENSE=HPND +RDEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-)] media-gfx/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] python_targets_pypy? ( virtual/pypy:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_3? ( >=dev-lang/python-3.3.2-r2:3.3 ) python_targets_python3_4? ( dev-lang/python:3.4 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-)] +REQUIRED_USE=|| ( python_targets_pypy python_targets_python2_7 python_targets_python3_3 python_targets_python3_4 ) +SLOT=0 +SRC_URI=http://www.biopython.org/DIST/biopython-1.65.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:distutils-r1 src_configure:distutils-r1 src_compile:distutils-r1 src_test:distutils-r1 src_install:distutils-r1 +_eclasses_=distutils-r1 4e8ac1ba76ddacd8f7c0289aa586a34c eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=ed3332b0c893b27c66efacb74b25fabd diff --git a/metadata/md5-cache/sci-biology/biopython-1.66 b/metadata/md5-cache/sci-biology/biopython-1.66 new file mode 100644 index 000000000000..29ba81e8407a --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopython-1.66 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] media-gfx/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] sys-devel/flex python_targets_pypy? ( virtual/pypy:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_3? ( >=dev-lang/python-3.3.2-r2:3.3 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +DESCRIPTION=Python modules for computational molecular biology +EAPI=5 +HOMEPAGE=http://www.biopython.org/ https://pypi.python.org/pypi/biopython/ +IUSE=python_targets_pypy python_targets_python2_7 python_targets_python3_3 python_targets_python3_4 python_targets_python3_5 +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux +LICENSE=HPND +RDEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_3(-)?,-python_single_target_python3_3(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] media-gfx/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] python_targets_pypy? ( virtual/pypy:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_3? ( >=dev-lang/python-3.3.2-r2:3.3 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +REQUIRED_USE=|| ( python_targets_pypy python_targets_python2_7 python_targets_python3_3 python_targets_python3_4 python_targets_python3_5 ) +SLOT=0 +SRC_URI=http://www.biopython.org/DIST/biopython-1.66.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:distutils-r1 src_configure:distutils-r1 src_compile:distutils-r1 src_test:distutils-r1 src_install:distutils-r1 +_eclasses_=distutils-r1 4e8ac1ba76ddacd8f7c0289aa586a34c eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3603e7d618d57e8df35f95bd62c52c56 diff --git a/metadata/md5-cache/sci-biology/bioruby-1.4.3.0001-r1 b/metadata/md5-cache/sci-biology/bioruby-1.4.3.0001-r1 new file mode 100644 index 000000000000..8a84ab1655e9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioruby-1.4.3.0001-r1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=test? ( ruby_targets_ruby20? ( dev-ruby/libxml[ruby_targets_ruby20] ) ) ruby_targets_ruby20? ( dev-lang/ruby:2.0 ) ruby_targets_ruby20? ( doc? ( dev-ruby/rake[ruby_targets_ruby20] ) ) ruby_targets_ruby20? ( test? ( dev-ruby/rake[ruby_targets_ruby20] ) ) ruby_targets_ruby20? ( virtual/rubygems[ruby_targets_ruby20] ) test? ( ruby_targets_ruby20? ( virtual/rubygems[ruby_targets_ruby20] ) ) +DESCRIPTION=An integrated environment for bioinformatics using the Ruby language +EAPI=5 +HOMEPAGE=http://www.bioruby.org/ +IUSE=test elibc_FreeBSD ruby_targets_ruby20 doc test test +KEYWORDS=amd64 ~ppc x86 +LICENSE=Ruby +RDEPEND=ruby_targets_ruby20? ( dev-ruby/libxml[ruby_targets_ruby20] ) ruby_targets_ruby20? ( dev-lang/ruby:2.0 ) ruby_targets_ruby20? ( virtual/rubygems[ruby_targets_ruby20] ) +REQUIRED_USE=|| ( ruby_targets_ruby20 ) +SLOT=0 +SRC_URI=http://www.bioruby.org/archive/bioruby-1.4.3.0001.tar.gz +_eclass_exported_funcs=pkg_setup:ruby-ng src_unpack:ruby-ng src_prepare:ruby-ng src_configure:ruby-ng src_compile:ruby-ng src_test:ruby-ng src_install:ruby-ng +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 ruby-fakegem 836f858624840907bbb6ae6f2c881cb7 ruby-ng 3b6431b487e69b5070a45ea20d1c4c6c ruby-utils 2f896785ed65442d7e84ab5f5eef3bd3 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=2b48b0bb84be40d6a0d45f6030a05821 diff --git a/metadata/md5-cache/sci-biology/bioruby-9999 b/metadata/md5-cache/sci-biology/bioruby-9999 new file mode 100644 index 000000000000..0a75ffde3b4b --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioruby-9999 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=test? ( ruby_targets_ruby20? ( dev-ruby/libxml[ruby_targets_ruby20] ) ) dev-vcs/git ruby_targets_ruby20? ( dev-lang/ruby:2.0 ) ruby_targets_ruby20? ( doc? ( dev-ruby/rake[ruby_targets_ruby20] ) ) ruby_targets_ruby20? ( test? ( dev-ruby/rake[ruby_targets_ruby20] ) ) ruby_targets_ruby20? ( virtual/rubygems[ruby_targets_ruby20] ) test? ( ruby_targets_ruby20? ( virtual/rubygems[ruby_targets_ruby20] ) ) +DESCRIPTION=An integrated environment for bioinformatics using the Ruby language +EAPI=5 +HOMEPAGE=http://www.bioruby.org/ +IUSE=test elibc_FreeBSD ruby_targets_ruby20 doc test test +LICENSE=Ruby +RDEPEND=ruby_targets_ruby20? ( dev-ruby/libxml[ruby_targets_ruby20] ) ruby_targets_ruby20? ( dev-lang/ruby:2.0 ) ruby_targets_ruby20? ( virtual/rubygems[ruby_targets_ruby20] ) +REQUIRED_USE=|| ( ruby_targets_ruby20 ) +SLOT=0 +_eclass_exported_funcs=pkg_setup:ruby-ng src_unpack:ruby-ng src_prepare:ruby-ng src_configure:ruby-ng src_compile:ruby-ng src_test:ruby-ng src_install:ruby-ng +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e git-2 672c3929a162f221a53b4ccb4d25d8a2 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 ruby-fakegem 836f858624840907bbb6ae6f2c881cb7 ruby-ng 3b6431b487e69b5070a45ea20d1c4c6c ruby-utils 2f896785ed65442d7e84ab5f5eef3bd3 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=f1c6444e37e5e84f077e43b84b1a2c75 diff --git a/metadata/md5-cache/sci-biology/biosql-1.0.1 b/metadata/md5-cache/sci-biology/biosql-1.0.1 new file mode 100644 index 000000000000..b799ba667cad --- /dev/null +++ b/metadata/md5-cache/sci-biology/biosql-1.0.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install postinst +DEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) +DESCRIPTION=A generic bioinformatics relational database model +EAPI=0 +HOMEPAGE=http://www.biosql.org/ +IUSE=mysql postgres +KEYWORDS=amd64 x86 +LICENSE=LGPL-3 +RDEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) +SLOT=0 +SRC_URI=http://biosql.org/DIST/biosql-1.0.1.tar.bz2 +_eclass_exported_funcs=pkg_postinst:- src_install:- +_md5_=81c48a17c4a95e2256f9e8408415fc81 diff --git a/metadata/md5-cache/sci-biology/blat-34 b/metadata/md5-cache/sci-biology/blat-34 new file mode 100644 index 000000000000..daa323695045 --- /dev/null +++ b/metadata/md5-cache/sci-biology/blat-34 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=app-arch/unzip +DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner +EAPI=0 +HOMEPAGE=http://www.cse.ucsc.edu/~kent/ +KEYWORDS=amd64 x86 +LICENSE=blat +SLOT=0 +SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip +_eclass_exported_funcs=src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=54aad31b5a90dc0387ba6c87ba539ff1 diff --git a/metadata/md5-cache/sci-biology/blat-34-r1 b/metadata/md5-cache/sci-biology/blat-34-r1 new file mode 100644 index 000000000000..d32816993f42 --- /dev/null +++ b/metadata/md5-cache/sci-biology/blat-34-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=app-arch/unzip +DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner +EAPI=4 +HOMEPAGE=http://www.cse.ucsc.edu/~kent/ +KEYWORDS=~amd64 ~x86 ~x64-macos +LICENSE=blat +SLOT=0 +SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2fb31e749261157d1329bfdeb6b73c6b diff --git a/metadata/md5-cache/sci-biology/blossoc-1.4.0 b/metadata/md5-cache/sci-biology/blossoc-1.4.0 new file mode 100644 index 000000000000..837cc52350ca --- /dev/null +++ b/metadata/md5-cache/sci-biology/blossoc-1.4.0 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sci-libs/gsl dev-libs/boost sci-biology/snpfile !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A linkage disequilibrium association mapping tool +EAPI=2 +HOMEPAGE=http://www.daimi.au.dk/~mailund/Blossoc/ +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=sci-libs/gsl dev-libs/boost sci-biology/snpfile +SLOT=0 +SRC_URI=http://www.daimi.au.dk/~mailund/Blossoc/download/blossoc-1.4.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=7d43b42d61abc20f34b19ce387a4f72d diff --git a/metadata/md5-cache/sci-biology/bowtie-1.1.2 b/metadata/md5-cache/sci-biology/bowtie-1.1.2 new file mode 100644 index 000000000000..166abb98cded --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-1.1.2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=app-arch/unzip tbb? ( dev-cpp/tbb ) +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=5 +HOMEPAGE=http://bowtie-bio.sourceforge.net/ +IUSE=examples +tbb +KEYWORDS=amd64 x86 ~x64-macos +LICENSE=Artistic +SLOT=1 +SRC_URI=mirror://sourceforge/bowtie-bio/bowtie-1.1.2-src.zip +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=bea647a3059e7392734895f8719da851 diff --git a/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 b/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 new file mode 100644 index 000000000000..dbe2e5540617 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare +DEPEND=tbb? ( dev-cpp/tbb ) sci-biology/seqan:1.4 app-arch/unzip +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=6 +HOMEPAGE=http://bowtie-bio.sourceforge.net/ +IUSE=examples +tbb +KEYWORDS=~amd64 ~x86 ~x64-macos +LICENSE=Artistic +RDEPEND=tbb? ( dev-cpp/tbb ) +SLOT=1 +SRC_URI=mirror://sourceforge/bowtie-bio/bowtie-1.1.2-src.zip +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3ffda47d0c02ed05ec45a657f7a10b19 diff --git a/metadata/md5-cache/sci-biology/bowtie-2.2.6 b/metadata/md5-cache/sci-biology/bowtie-2.2.6 new file mode 100644 index 000000000000..2b42a811bbf9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-2.2.6 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install pretend +DEPEND=dev-lang/perl app-arch/unzip tbb? ( dev-cpp/tbb ) +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=5 +HOMEPAGE=http://bowtie-bio.sourceforge.net/bowtie2/ +IUSE=examples cpu_flags_x86_sse2 +tbb +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=dev-lang/perl +SLOT=2 +SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.2.6/bowtie2-2.2.6-source.zip +_eclass_exported_funcs=pkg_pretend:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=5f8bf2d3f475b2c4c9d96b62096f7ab7 diff --git a/metadata/md5-cache/sci-biology/bowtie-2.2.8 b/metadata/md5-cache/sci-biology/bowtie-2.2.8 new file mode 100644 index 000000000000..8833594e2bbb --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-2.2.8 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install pretend +DEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) app-arch/unzip +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=6 +HOMEPAGE=http://bowtie-bio.sourceforge.net/bowtie2/ +IUSE=examples cpu_flags_x86_sse2 +tbb +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) +SLOT=2 +SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.2.8/bowtie2-2.2.8-source.zip +_eclass_exported_funcs=pkg_pretend:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=7dd8090b15e166773555054785056f3f diff --git a/metadata/md5-cache/sci-biology/bwa-0.7.12 b/metadata/md5-cache/sci-biology/bwa-0.7.12 new file mode 100644 index 000000000000..2cd1f29f9875 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bwa-0.7.12 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner +EAPI=5 +HOMEPAGE=http://bio-bwa.sourceforge.net/ +KEYWORDS=amd64 x86 ~x64-macos +LICENSE=GPL-3 +SLOT=0 +SRC_URI=mirror://sourceforge/bio-bwa/bwa-0.7.12.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=fcc20ae2280da350669d2a27a7625237 diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.5.1 b/metadata/md5-cache/sci-biology/cd-hit-4.5.1 new file mode 100644 index 000000000000..3d2f14524425 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cd-hit-4.5.1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare setup +DESCRIPTION=Clustering Database at High Identity with Tolerance +EAPI=3 +HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ +IUSE=openmp +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://cdhit.googlecode.com/files/cd-hit-v4.5.1-2011-01-31.tgz +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2219ae002375618957700246d19245ee diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.5.4 b/metadata/md5-cache/sci-biology/cd-hit-4.5.4 new file mode 100644 index 000000000000..b2a28346bdf9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cd-hit-4.5.4 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare setup +DESCRIPTION=Clustering Database at High Identity with Tolerance +EAPI=4 +HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ +IUSE=openmp +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://cdhit.googlecode.com/files/cd-hit-v4.5.4-2011-03-07.tgz +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2341c46a3e214cc187e24ee6e9619a28 diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.6 b/metadata/md5-cache/sci-biology/cd-hit-4.6 new file mode 100644 index 000000000000..7c980a34fb73 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cd-hit-4.6 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare setup +DESCRIPTION=Clustering Database at High Identity with Tolerance +EAPI=4 +HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ +IUSE=doc openmp +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://cdhit.googlecode.com/files/cd-hit-v4.6-2012-04-25.tgz +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=8a2e925af92a3450f7d695bc78112d38 diff --git a/metadata/md5-cache/sci-biology/clustal-omega-1.2.1 b/metadata/md5-cache/sci-biology/clustal-omega-1.2.1 new file mode 100644 index 000000000000..2ddad416dc95 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustal-omega-1.2.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-libs/argtable !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Scalable multiple alignment of protein sequences +EAPI=5 +HOMEPAGE=http://www.clustal.org/omega/ +IUSE=static-libs +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=dev-libs/argtable +SLOT=0 +SRC_URI=http://www.clustal.org/omega/clustal-omega-1.2.1.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:autotools-utils src_compile:autotools-utils src_test:autotools-utils src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=4e27f76eeb748a11d818033236165609 diff --git a/metadata/md5-cache/sci-biology/clustalw-1.83-r3 b/metadata/md5-cache/sci-biology/clustalw-1.83-r3 new file mode 100644 index 000000000000..b9395f44f3b7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-1.83-r3 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=5 +HOMEPAGE=http://www.embl-heidelberg.de/~seqanal/ +KEYWORDS=alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=clustalw +SLOT=1 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.83.UNIX.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=d3c4e4fe400e259421328a7aed1776d9 diff --git a/metadata/md5-cache/sci-biology/clustalw-2.1 b/metadata/md5-cache/sci-biology/clustalw-2.1 new file mode 100644 index 000000000000..5ec0520dcde0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-2.1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=- +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=4 +HOMEPAGE=http://www.clustal.org/ +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-3 LGPL-3 +SLOT=2 +SRC_URI=http://www.clustal.org/download/current/clustalw-2.1.tar.gz +_eclass_exported_funcs=- +_md5_=ae716317d0a8d5852664b851af147286 diff --git a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r1 b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r1 new file mode 100644 index 000000000000..79e194fb0376 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=install prepare +DEPEND=virtual/mpi +DESCRIPTION=A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm +EAPI=4 +HOMEPAGE=http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php +IUSE=mpi_njtree static_pairalign +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=virtual/mpi +SLOT=0 +SRC_URI=http://web.bii.a-star.edu.sg/~kuobin/clustalw-mpi/clustalw-mpi-0.13.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=35aeabe13c3f17845ebe48287b554312 diff --git a/metadata/md5-cache/sci-biology/clustalx-2.1-r1 b/metadata/md5-cache/sci-biology/clustalx-2.1-r1 new file mode 100644 index 000000000000..5cc0e5a04e62 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalx-2.1-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare unpack +DEPEND=dev-qt/qtcore:4 dev-qt/qtgui:4 +DESCRIPTION=Graphical interface for the ClustalW multiple alignment program +EAPI=5 +HOMEPAGE=http://www.ebi.ac.uk/tools/clustalw2/ +KEYWORDS=amd64 x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=dev-qt/qtcore:4 dev-qt/qtgui:4 >=sci-biology/clustalw-2.1 +SLOT=0 +SRC_URI=http://www.clustal.org/download/current/clustalx-2.1.tar.gz +_eclass_exported_funcs=src_unpack:qt4-r2 src_prepare:- src_configure:qt4-r2 src_compile:qt4-r2 src_install:- +_eclasses_=base 3fe4f8980633fd7bc69e9887209ba2fe eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 qmake-utils 0a242e7177789b0028b4045f336dd4db qt4-r2 d6c113024bb3086a1facc65cd338930e toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=46a1492fe4bfbbe5e2adc7a94fe7d5a6 diff --git a/metadata/md5-cache/sci-biology/consed-19-r2 b/metadata/md5-cache/sci-biology/consed-19-r2 new file mode 100644 index 000000000000..0399c81511ad --- /dev/null +++ b/metadata/md5-cache/sci-biology/consed-19-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install postinst prepare +DEPEND=>=x11-libs/motif-2.3:0 +DESCRIPTION=A genome sequence finishing program +EAPI=3 +HOMEPAGE=http://bozeman.mbt.washington.edu/consed/consed.html +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RDEPEND=>=x11-libs/motif-2.3:0 >=sci-biology/phred-000925 >=sci-biology/phrap-1.080721 +RESTRICT=fetch +SLOT=0 +SRC_URI=consed-19-sources.tar.gz consed-19-linux.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=87bace678f02004b19b2ab3b4e392aad diff --git a/metadata/md5-cache/sci-biology/consed-27 b/metadata/md5-cache/sci-biology/consed-27 new file mode 100644 index 000000000000..c063724e9c78 --- /dev/null +++ b/metadata/md5-cache/sci-biology/consed-27 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install postinst prepare +DEPEND=>=x11-libs/motif-2.3:0 +DESCRIPTION=A genome sequence finishing program +EAPI=5 +HOMEPAGE=http://bozeman.mbt.washington.edu/consed/consed.html +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RDEPEND=>=x11-libs/motif-2.3:0 sci-biology/samtools >=sci-biology/phred-000925 >=sci-biology/phrap-1.080721 dev-lang/perl +RESTRICT=fetch +SLOT=0 +SRC_URI=consed-27-sources.tar.gz consed-27-linux.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=aacf6ebdd167286a4e3ffcb214152b9b diff --git a/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 b/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 new file mode 100644 index 000000000000..48ba0c37955c --- /dev/null +++ b/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare +DEPEND=sci-biology/samtools:0.1-legacy >=dev-libs/boost-1.59.0:= dev-cpp/eigen:3 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Transcript assembly and differential expression/regulation for RNA-Seq +EAPI=6 +HOMEPAGE=http://cufflinks.cbcb.umd.edu/ +IUSE=debug +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=sci-biology/samtools:0.1-legacy >=dev-libs/boost-1.59.0:= dev-cpp/eigen:3 +SLOT=0 +SRC_URI=http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6b93e6dbae7355a08affefe4c39cf8dc diff --git a/metadata/md5-cache/sci-biology/cutg-160-r1 b/metadata/md5-cache/sci-biology/cutg-160-r1 new file mode 100644 index 000000000000..adb97d0f3c88 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cutg-160-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=Codon usage tables calculated from GenBank +EAPI=5 +HOMEPAGE=http://www.kazusa.or.jp/codon/ +IUSE=emboss minimal +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/cutg-160.tar.xz +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=8841e19b9fa19461b5074b6156cf819c diff --git a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r1 b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r1 new file mode 100644 index 000000000000..aa0764c6cc6b --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Greedy and progressive approaches for segment-based multiple sequence alignment +EAPI=5 +HOMEPAGE=http://dialign-tx.gobics.de/ +KEYWORDS=amd64 x86 +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=bebacda7b9082951500b83768cf250d1 diff --git a/metadata/md5-cache/sci-biology/dialign2-2.2.1 b/metadata/md5-cache/sci-biology/dialign2-2.2.1 new file mode 100644 index 000000000000..ed7462551333 --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign2-2.2.1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DESCRIPTION=Multiple sequence alignment +EAPI=5 +HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz +_eclass_exported_funcs=src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=ee98e826a5b57d9ea610cda6d19929da diff --git a/metadata/md5-cache/sci-biology/diya-1.0_rc4 b/metadata/md5-cache/sci-biology/diya-1.0_rc4 new file mode 100644 index 000000000000..c72251a28988 --- /dev/null +++ b/metadata/md5-cache/sci-biology/diya-1.0_rc4 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple dev-lang/perl:=[-build(-)] +DESCRIPTION=Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotation +EAPI=5 +HOMEPAGE=http://gmod.org/wiki/Diya +IUSE=-minimal +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple !minimal? ( sci-biology/mummer sci-biology/glimmer sci-biology/trnascan-se sci-biology/infernal ) dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=mirror://sourceforge/diyg/files/diya/diya-1.0/diya-1.0-rc4.tar.gz +_eclass_exported_funcs=src_unpack:perl-module src_prepare:perl-module src_configure:perl-module src_compile:perl-module src_test:perl-module src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=fa0fc42a99b6d4398e74da15f5fa8b3e diff --git a/metadata/md5-cache/sci-biology/elph-0.1.5 b/metadata/md5-cache/sci-biology/elph-0.1.5 new file mode 100644 index 000000000000..55fd5b260917 --- /dev/null +++ b/metadata/md5-cache/sci-biology/elph-0.1.5 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install unpack +DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program +EAPI=0 +HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ +KEYWORDS=x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-0.1.5.tar.gz +_eclass_exported_funcs=src_unpack:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=fd17c47a2e8f2da8e6c3236a9e7dec89 diff --git a/metadata/md5-cache/sci-biology/elph-1.0.1 b/metadata/md5-cache/sci-biology/elph-1.0.1 new file mode 100644 index 000000000000..6aea6b537004 --- /dev/null +++ b/metadata/md5-cache/sci-biology/elph-1.0.1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program +EAPI=0 +HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-1.0.1.tar.gz +_eclass_exported_funcs=src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=57736c0fadfb9a7f58d7b479b2ccecc6 diff --git a/metadata/md5-cache/sci-biology/embassy-6.6.0 b/metadata/md5-cache/sci-biology/embassy-6.6.0 new file mode 100644 index 000000000000..799106987754 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-6.6.0 @@ -0,0 +1,10 @@ +DEFINED_PHASES=- +DESCRIPTION=A meta-package for installing all EMBASSY packages (EMBOSS add-ons) +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/embassy/ +KEYWORDS=amd64 x86 ~x86-linux ~ppc-macos +LICENSE=freedist +RDEPEND=>=sci-biology/embassy-cbstools-1.0.0.650 >=sci-biology/embassy-clustalomega-1.1.0 >=sci-biology/embassy-domainatrix-0.1.650 >=sci-biology/embassy-domalign-0.1.650 >=sci-biology/embassy-domsearch-0.1.650 >=sci-biology/embassy-emnu-1.05.650 >=sci-biology/embassy-esim4-1.0.0.650 >=sci-biology/embassy-hmmer-2.3.2.650 >=sci-biology/embassy-iprscan-4.3.1.650 >=sci-biology/embassy-meme-4.7.650 >=sci-biology/embassy-mse-3.0.0.650 >=sci-biology/embassy-phylipnew-3.69.650 >=sci-biology/embassy-signature-0.1.650 >=sci-biology/embassy-structure-0.1.650 >=sci-biology/embassy-topo-2.0.650 >=sci-biology/embassy-vienna-1.7.2.650 +SLOT=0 +_eclass_exported_funcs=- +_md5_=d816608e82acbfc4dde275f13af65181 diff --git a/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.650 b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.650 new file mode 100644 index 000000000000..aa4ca25ed075 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Applications from the CBS group +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.650.tar.gz -> embassy-cbstools-1.0.0.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=186a646a01796d80e96382eda18890f6 diff --git a/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0 b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0 new file mode 100644 index 000000000000..bfc9580106c8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Clustal Omega - Scalable multiple protein sequences alignment +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/clustal-omega dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-1.1.0.tar.gz -> embassy-clustalomega-1.1.0.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=78d217460299d444dd47ef25eccc6780 diff --git a/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.650 b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.650 new file mode 100644 index 000000000000..5a7fcbbc5693 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain analysis add-on package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.650.tar.gz -> embassy-domainatrix-0.1.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=63b5b0b16a577be381e2872c78742942 diff --git a/metadata/md5-cache/sci-biology/embassy-domalign-0.1.650 b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.650 new file mode 100644 index 000000000000..c4e9fcb1f59e --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain alignment add-on package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.650.tar.gz -> embassy-domalign-0.1.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=af2fa82680f0057751ab091d1c0de659 diff --git a/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.650 b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.650 new file mode 100644 index 000000000000..5b6e3652d57c --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain search add-on package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.650.tar.gz -> embassy-domsearch-0.1.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=4f3855b8861141c88bf0c4c267e34074 diff --git a/metadata/md5-cache/sci-biology/embassy-emnu-1.05.650-r1 b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.650-r1 new file mode 100644 index 000000000000..9ab47fe67981 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.650-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Simple menu of EMBOSS applications +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=ncurses mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=ncurses? ( sys-libs/ncurses:= ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.650.tar.gz -> embassy-emnu-1.05.650-r1.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:- src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=8dbc38e69d33e3dab2515755b7bdb388 diff --git a/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.650 b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.650 new file mode 100644 index 000000000000..2d3dbca5294a --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.650.tar.gz -> embassy-esim4-1.0.0.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=372a55d64865de9d88f2b796cfe2c8e6 diff --git a/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.650 b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.650 new file mode 100644 index 000000000000..3a07f4de8276 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Wrappers for HMMER - Biological sequence analysis with profile HMMs +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/hmmer dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.650.tar.gz -> embassy-hmmer-2.3.2.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=b64d4a79867d45d7cc2bad22451b0d0b diff --git a/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.650 b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.650 new file mode 100644 index 000000000000..05d78e376d85 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of InterProScan motif detection add-on package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.650.tar.gz -> embassy-iprscan-4.3.1.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2be3be220e11153b8999ac69cad1485c diff --git a/metadata/md5-cache/sci-biology/embassy-meme-4.7.650 b/metadata/md5-cache/sci-biology/embassy-meme-4.7.650 new file mode 100644 index 000000000000..b82c83126ce3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-meme-4.7.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Wrappers for MEME - Multiple Em for Motif Elicitation +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/meme dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.7.650.tar.gz -> embassy-meme-4.7.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=aeca403317a95de25a390eef8bc0d435 diff --git a/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.650 b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.650 new file mode 100644 index 000000000000..5bb4f9919f90 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of MSE - Multiple Sequence Screen Editor +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=ncurses mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=ncurses? ( sys-libs/ncurses ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.650.tar.gz -> embassy-mse-3.0.0.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:- src_compile:autotools-utils src_test:autotools-utils src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=c282ceaf2e8cc53eba54fac7023c9a60 diff --git a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.650 b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.650 new file mode 100644 index 000000000000..cb3fd394d0cb --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of The Phylogeny Inference Package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 freedist +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.650.tar.gz -> embassy-phylipnew-3.69.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=27ce1ba3779bb97b11294e369862e616 diff --git a/metadata/md5-cache/sci-biology/embassy-signature-0.1.650 b/metadata/md5-cache/sci-biology/embassy-signature-0.1.650 new file mode 100644 index 000000000000..d71752ceaa00 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-signature-0.1.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein signature add-on package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.650.tar.gz -> embassy-signature-0.1.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=5dac08ee358b394884c4fe4b53a1f065 diff --git a/metadata/md5-cache/sci-biology/embassy-structure-0.1.650 b/metadata/md5-cache/sci-biology/embassy-structure-0.1.650 new file mode 100644 index 000000000000..823ae24bb7cc --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-structure-0.1.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein structure add-on package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.650.tar.gz -> embassy-structure-0.1.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=a6af3b3439050d2ecb65956c012c92ba diff --git a/metadata/md5-cache/sci-biology/embassy-topo-2.0.650 b/metadata/md5-cache/sci-biology/embassy-topo-2.0.650 new file mode 100644 index 000000000000..f469910f8b85 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-topo-2.0.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Transmembrane protein display +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.650.tar.gz -> embassy-topo-2.0.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=0edf6a1e13a42a6a8bc4050386b71ddd diff --git a/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.650 b/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.650 new file mode 100644 index 000000000000..ebcaae934ccd --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.650 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Vienna RNA package - RNA folding +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.650.tar.gz -> embassy-vienna-1.7.2.650.tar.gz +_eclass_exported_funcs=src_prepare:emboss-r1 src_configure:- src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=ebea12eb95dc9f0deba32a8853c44f7c diff --git a/metadata/md5-cache/sci-biology/emboss-6.6.0 b/metadata/md5-cache/sci-biology/emboss-6.6.0 new file mode 100644 index 000000000000..acde73355ff2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/emboss-6.6.0 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +DESCRIPTION=The European Molecular Biology Open Software Suite - A sequence analysis package +EAPI=5 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=minimal mysql pdf png postgres static-libs X +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0 +PDEPEND=!minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/primer3 sci-biology/prints sci-biology/prosite sci-biology/rebase ) +RDEPEND=!sys-devel/cons dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu ) png? ( media-libs/gd[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz +_eclass_exported_funcs=pkg_postinst:readme.gentoo src_prepare:emboss-r1 src_configure:emboss-r1 src_compile:autotools-utils src_test:autotools-utils src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb emboss-r1 4845d0df55fa82758c20d0fb0ef1a2a2 eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 readme.gentoo df3fc8fdaf5a519e7d48c83e7592c95f toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3905696a6d1cafc9d095d9da24e8a7ad diff --git a/metadata/md5-cache/sci-biology/eugene-4.1 b/metadata/md5-cache/sci-biology/eugene-4.1 new file mode 100644 index 000000000000..f95d3aaa5a22 --- /dev/null +++ b/metadata/md5-cache/sci-biology/eugene-4.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=prepare +DEPEND=media-libs/gd[png] media-libs/libpng:0= !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Eukaryotic gene predictor +EAPI=5 +HOMEPAGE=http://www.inra.fr/mia/T/EuGene/ +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=media-libs/gd[png] media-libs/libpng:0= +RESTRICT=test +SLOT=0 +SRC_URI=https://mulcyber.toulouse.inra.fr/frs/download.php/1157/eugene-4.1.tar.gz +_eclass_exported_funcs=src_prepare:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=f64907e857ca8ed5db03a3315cc74e33 diff --git a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r1 b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r1 new file mode 100644 index 000000000000..d0a1512972b9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-libs/glib:2 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Generic tool for pairwise sequence comparison +EAPI=4 +HOMEPAGE=http://www.ebi.ac.uk/~guy/exonerate/ +IUSE=utils test threads +KEYWORDS=~amd64 ~x86 ~ppc-macos ~x64-macos +LICENSE=GPL-3 +RDEPEND=dev-libs/glib:2 +REQUIRED_USE=test? ( utils ) +SLOT=0 +SRC_URI=http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- src_compile:autotools-utils src_test:autotools-utils src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=178b12fcf2b0c150e6145c1d28525a7b diff --git a/metadata/md5-cache/sci-biology/express-0.9.5 b/metadata/md5-cache/sci-biology/express-0.9.5 new file mode 100644 index 000000000000..2369217498b8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/express-0.9.5 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-libs/boost sys-libs/zlib sci-biology/bamtools sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=Streaming RNA-Seq Analysis +EAPI=4 +HOMEPAGE=http://bio.math.berkeley.edu/eXpress/ +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=dev-libs/boost sys-libs/zlib sci-biology/bamtools +SLOT=0 +SRC_URI=http://bio.math.berkeley.edu/eXpress/downloads/express-0.9.5/express-0.9.5-src.tgz +_eclass_exported_funcs=src_prepare:- src_configure:cmake-utils src_compile:cmake-utils src_test:cmake-utils src_install:cmake-utils +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=010fdb416bdadb2983034b01eb9b8f58 diff --git a/metadata/md5-cache/sci-biology/express-0.9.5-r1 b/metadata/md5-cache/sci-biology/express-0.9.5-r1 new file mode 100644 index 000000000000..c2486f75e53d --- /dev/null +++ b/metadata/md5-cache/sci-biology/express-0.9.5-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=dev-libs/boost-1.52.0:= sys-libs/zlib sci-biology/bamtools sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=Streaming RNA-Seq Analysis +EAPI=5 +HOMEPAGE=http://bio.math.berkeley.edu/eXpress/ +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=>=dev-libs/boost-1.52.0:= sys-libs/zlib sci-biology/bamtools +SLOT=0 +SRC_URI=http://bio.math.berkeley.edu/eXpress/downloads/express-0.9.5/express-0.9.5-src.tgz +_eclass_exported_funcs=src_prepare:- src_configure:cmake-utils src_compile:cmake-utils src_test:cmake-utils src_install:cmake-utils +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=3bc7636082b31abb4ab2b71a0a941a81 diff --git a/metadata/md5-cache/sci-biology/express-1.5.1 b/metadata/md5-cache/sci-biology/express-1.5.1 new file mode 100644 index 000000000000..fd3ce9c4595c --- /dev/null +++ b/metadata/md5-cache/sci-biology/express-1.5.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=dev-libs/boost-1.52.0:= dev-libs/protobuf dev-util/google-perftools sys-libs/zlib sci-biology/bamtools sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=Streaming RNA-Seq Analysis +EAPI=5 +HOMEPAGE=http://bio.math.berkeley.edu/eXpress/ +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=>=dev-libs/boost-1.52.0:= dev-libs/protobuf dev-util/google-perftools sys-libs/zlib sci-biology/bamtools +SLOT=0 +SRC_URI=http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz +_eclass_exported_funcs=src_prepare:cmake-utils src_configure:- src_compile:cmake-utils src_test:cmake-utils src_install:cmake-utils +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=c2f687191454c4316a3ee0917423a42f diff --git a/metadata/md5-cache/sci-biology/fasta-35.4.10 b/metadata/md5-cache/sci-biology/fasta-35.4.10 new file mode 100644 index 000000000000..94ff00360a89 --- /dev/null +++ b/metadata/md5-cache/sci-biology/fasta-35.4.10 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=test? ( app-shells/tcsh ) +DESCRIPTION=FASTA is a DNA and Protein sequence alignment software package +EAPI=2 +HOMEPAGE=http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml +IUSE=debug cpu_flags_x86_sse2 test +KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos +LICENSE=fasta +SLOT=0 +SRC_URI=http://faculty.virginia.edu/wrpearson/fasta/fasta3/fasta-35.4.10.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=45693968b9680c3c6bfd9a05d54dc62a diff --git a/metadata/md5-cache/sci-biology/fasta-36.3.5e b/metadata/md5-cache/sci-biology/fasta-36.3.5e new file mode 100644 index 000000000000..beae54931ee2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/fasta-36.3.5e @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=test? ( app-shells/tcsh ) +DESCRIPTION=FASTA is a DNA and Protein sequence alignment software package +EAPI=5 +HOMEPAGE=http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml +IUSE=debug cpu_flags_x86_sse2 test +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos +LICENSE=fasta +SLOT=0 +SRC_URI=http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.5e.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3f2fe79adf516da76e4ecbb185cad0bc diff --git a/metadata/md5-cache/sci-biology/fasttree-2.1.7 b/metadata/md5-cache/sci-biology/fasttree-2.1.7 new file mode 100644 index 000000000000..aa040e55ba9d --- /dev/null +++ b/metadata/md5-cache/sci-biology/fasttree-2.1.7 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=Fast inference of approximately-maximum-likelihood phylogenetic trees +EAPI=5 +HOMEPAGE=http://www.microbesonline.org/fasttree/ +IUSE=double-precision openmp cpu_flags_x86_sse3 +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +REQUIRED_USE=?? ( double-precision cpu_flags_x86_sse3 ) +SLOT=0 +SRC_URI=http://www.microbesonline.org/fasttree/FastTree-2.1.7.c http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-2.1.7.c http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-2.1.7.tar.gz +_eclass_exported_funcs=src_unpack:- src_prepare:- src_configure:- src_compile:cmake-utils src_test:cmake-utils src_install:cmake-utils +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=61aa89b01dafa750683148d15dde6e52 diff --git a/metadata/md5-cache/sci-biology/fasttree-2.1.8 b/metadata/md5-cache/sci-biology/fasttree-2.1.8 new file mode 100644 index 000000000000..9f597238e601 --- /dev/null +++ b/metadata/md5-cache/sci-biology/fasttree-2.1.8 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=Fast inference of approximately-maximum-likelihood phylogenetic trees +EAPI=5 +HOMEPAGE=http://www.microbesonline.org/fasttree/ +IUSE=double-precision openmp cpu_flags_x86_sse3 +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +REQUIRED_USE=?? ( double-precision cpu_flags_x86_sse3 ) +SLOT=0 +SRC_URI=http://www.microbesonline.org/fasttree/FastTree-2.1.8.c http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-2.1.8.c http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-2.1.8.tar.gz +_eclass_exported_funcs=src_unpack:- src_prepare:- src_configure:- src_compile:cmake-utils src_test:cmake-utils src_install:cmake-utils +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=a57c162d671d45c02f889b16b5bdb38e diff --git a/metadata/md5-cache/sci-biology/finchtv-1.3.1-r2 b/metadata/md5-cache/sci-biology/finchtv-1.3.1-r2 new file mode 100644 index 000000000000..46f84c78f329 --- /dev/null +++ b/metadata/md5-cache/sci-biology/finchtv-1.3.1-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=Graphical viewer for chromatogram files +EAPI=5 +HOMEPAGE=http://www.geospiza.com/finchtv/ +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=finchtv +SLOT=0 +SRC_URI=http://www.geospiza.com/finchtv/download/programs/linux/finchtv_1_3_1.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=316fe22af17aef54b898e9b8620e47e1 diff --git a/metadata/md5-cache/sci-biology/foldingathome-7.3.6-r2 b/metadata/md5-cache/sci-biology/foldingathome-7.3.6-r2 new file mode 100644 index 000000000000..606166434b6d --- /dev/null +++ b/metadata/md5-cache/sci-biology/foldingathome-7.3.6-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install postinst postrm preinst setup +DESCRIPTION=Folding@Home is a distributed computing project for protein folding +EAPI=4 +HOMEPAGE=http://folding.stanford.edu/FAQ-SMP.html +KEYWORDS=~amd64 ~x86 +LICENSE=FAH-EULA-2009 FAH-special-permission +RDEPEND=app-arch/bzip2 sys-devel/gcc sys-libs/glibc sys-libs/zlib +RESTRICT=mirror bindist strip +SLOT=0 +SRC_URI=x86? ( https://fah.stanford.edu/file-releases/public/release/fahclient/centos-5.5-32bit/v7.3/fahclient_7.3.6-32bit-release.tar.bz2 ) amd64? ( https://fah.stanford.edu/file-releases/public/release/fahclient/centos-5.3-64bit/v7.3/fahclient_7.3.6-64bit-release.tar.bz2 ) +_eclass_exported_funcs=pkg_preinst:- pkg_postrm:- pkg_postinst:- pkg_setup:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb user 906f3c8eb3a2350a4f1191a89baa3e46 versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=3c0aaea43823b5adf947c6a0e5090ec3 diff --git a/metadata/md5-cache/sci-biology/foldingathome-7.4.4 b/metadata/md5-cache/sci-biology/foldingathome-7.4.4 new file mode 100644 index 000000000000..0aa08b64800c --- /dev/null +++ b/metadata/md5-cache/sci-biology/foldingathome-7.4.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install postinst postrm preinst setup +DESCRIPTION=Folding@Home is a distributed computing project for protein folding +EAPI=4 +HOMEPAGE=http://folding.stanford.edu/FAQ-SMP.html +KEYWORDS=~amd64 ~x86 +LICENSE=FAH-EULA-2014 FAH-special-permission +RDEPEND=app-arch/bzip2 sys-devel/gcc sys-libs/glibc sys-libs/zlib +RESTRICT=mirror bindist strip +SLOT=0 +SRC_URI=x86? ( https://fah.stanford.edu/file-releases/public/release/fahclient/centos-5.5-32bit/v7.4/fahclient_7.4.4-32bit-release.tar.bz2 ) amd64? ( https://fah.stanford.edu/file-releases/public/release/fahclient/centos-5.3-64bit/v7.4/fahclient_7.4.4-64bit-release.tar.bz2 ) +_eclass_exported_funcs=pkg_preinst:- pkg_postrm:- pkg_postinst:- pkg_setup:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb user 906f3c8eb3a2350a4f1191a89baa3e46 versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=9242ae0fc742c83a08f28417712e5fe3 diff --git a/metadata/md5-cache/sci-biology/gatk-2.4 b/metadata/md5-cache/sci-biology/gatk-2.4 new file mode 100644 index 000000000000..4306bb335a82 --- /dev/null +++ b/metadata/md5-cache/sci-biology/gatk-2.4 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install preinst prepare setup unpack +DEPEND=>=virtual/jdk-1.6 >=dev-java/java-config-2.2.0 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=The Genome Analysis Toolkit +EAPI=5 +HOMEPAGE=http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit +IUSE=elibc_FreeBSD elibc_FreeBSD +KEYWORDS=~amd64 +LICENSE=MIT +RDEPEND=>=virtual/jre-1.6 >=dev-java/java-config-2.2.0 +SLOT=0 +SRC_URI=https://github.com/broadgsa/gatk/archive/2.4.tar.gz -> gatk-2.4.tar.gz +_eclass_exported_funcs=pkg_preinst:java-pkg-2 pkg_setup:java-pkg-2 src_unpack:vcs-snapshot src_prepare:- src_configure:java-ant-2 src_compile:java-pkg-2 src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-2 b02dc1e46b3648e467b5fbdf7857cf28 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb vcs-snapshot b45be87e7012be0af8424e8a5644da1d versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=6e7edd964ee7eedfb9d0941dd49b840e diff --git a/metadata/md5-cache/sci-biology/gatk-9999 b/metadata/md5-cache/sci-biology/gatk-9999 new file mode 100644 index 000000000000..f372d090f765 --- /dev/null +++ b/metadata/md5-cache/sci-biology/gatk-9999 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install preinst prepare setup unpack +DEPEND=>=virtual/jdk-1.6 dev-vcs/git dev-vcs/git >=dev-java/java-config-2.2.0 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=The Genome Analysis Toolkit +EAPI=5 +HOMEPAGE=http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit +IUSE=elibc_FreeBSD elibc_FreeBSD +LICENSE=MIT +RDEPEND=>=virtual/jre-1.6 >=dev-java/java-config-2.2.0 +SLOT=0 +_eclass_exported_funcs=pkg_preinst:java-pkg-2 pkg_setup:java-pkg-2 src_unpack:git-2 src_prepare:- src_configure:java-ant-2 src_compile:java-pkg-2 src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e git-2 672c3929a162f221a53b4ccb4d25d8a2 java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-2 b02dc1e46b3648e467b5fbdf7857cf28 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=87fbeadb7427c25b13f5837263f8939f diff --git a/metadata/md5-cache/sci-biology/gibbs-3.1 b/metadata/md5-cache/sci-biology/gibbs-3.1 new file mode 100644 index 000000000000..b9206949d96f --- /dev/null +++ b/metadata/md5-cache/sci-biology/gibbs-3.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 ) !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Identify motifs, conserved regions, in DNA or protein sequences +EAPI=4 +HOMEPAGE=http://bayesweb.wadsworth.org/gibbs/gibbs.html +IUSE=mpi +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 ) +SLOT=0 +SRC_URI=mirror://gentoo/gibbs-3.1.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_configure:- src_compile:autotools-utils src_test:autotools-utils src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3330594e03e29a02e3796906b02101a9 diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02-r3 b/metadata/md5-cache/sci-biology/glimmer-3.02-r3 new file mode 100644 index 000000000000..b451165572e8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmer-3.02-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=An HMM-based microbial gene finding system from TIGR +EAPI=5 +HOMEPAGE=http://www.cbcb.umd.edu/software/glimmer/ +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh +SLOT=0 +SRC_URI=http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=e88e62a74099bfe5158b5dcc02b5b282 diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02b b/metadata/md5-cache/sci-biology/glimmer-3.02b new file mode 100644 index 000000000000..054f84138bad --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmer-3.02b @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=An HMM-based microbial gene finding system from TIGR +EAPI=5 +HOMEPAGE=http://ccb.jhu.edu/software/glimmer +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh sci-biology/elph +SLOT=0 +SRC_URI=http://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=0548d7bfa5d5a7de4e2265a7038e3c0b diff --git a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 new file mode 100644 index 000000000000..4b2d44a805c8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare unpack +DESCRIPTION=A eukaryotic gene finding system from TIGR +EAPI=4 +HOMEPAGE=http://www.cbcb.umd.edu/software/GlimmerHMM/ +KEYWORDS=amd64 x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.1.tar.gz +_eclass_exported_funcs=src_unpack:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=b42c827c4d6dc5e11c3d97315cf87522 diff --git a/metadata/md5-cache/sci-biology/gmap-2011.10.07 b/metadata/md5-cache/sci-biology/gmap-2011.10.07 new file mode 100644 index 000000000000..be25429940f4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/gmap-2011.10.07 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install test +DEPEND=samtools? ( sci-biology/samtools ) goby? ( sci-biology/goby-cpp ) +DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences +EAPI=2 +HOMEPAGE=http://www.gene.com/share/gmap/ +IUSE=+samtools +goby +KEYWORDS=~amd64 ~x86 +LICENSE=gmap +RDEPEND=samtools? ( sci-biology/samtools ) goby? ( sci-biology/goby-cpp ) +SLOT=0 +SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2011-10-07.tar.gz +_eclass_exported_funcs=src_configure:- src_test:- src_install:- +_md5_=bb56e8ff7b6d437c2070ea6870ea705e diff --git a/metadata/md5-cache/sci-biology/gmap-2012.07.20 b/metadata/md5-cache/sci-biology/gmap-2012.07.20 new file mode 100644 index 000000000000..8bd18249eb56 --- /dev/null +++ b/metadata/md5-cache/sci-biology/gmap-2012.07.20 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install test +DEPEND=samtools? ( sci-biology/samtools ) goby? ( sci-biology/goby-cpp ) +DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences +EAPI=4 +HOMEPAGE=http://research-pub.gene.com/gmap/ +IUSE=+samtools +goby +KEYWORDS=~amd64 ~x86 +LICENSE=gmap +RDEPEND=samtools? ( sci-biology/samtools ) goby? ( sci-biology/goby-cpp ) +SLOT=0 +SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.tar.gz +_eclass_exported_funcs=src_configure:- src_test:- src_install:- +_md5_=0d5226b6bcb4dbe94a4bfbc8b54f9aa7 diff --git a/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 new file mode 100644 index 000000000000..c88b03c7f9ae --- /dev/null +++ b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 @@ -0,0 +1,11 @@ +DEFINED_PHASES=- +DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences +EAPI=6 +HOMEPAGE=http://research-pub.gene.com/gmap/ +KEYWORDS=~amd64 ~x86 +LICENSE=gmap +SLOT=0 +SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2015-12-31.v5.tar.gz +_eclass_exported_funcs=- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=cb95c1947d1ab705cdf541bd023bbab0 diff --git a/metadata/md5-cache/sci-biology/goby-1.9.7.3 b/metadata/md5-cache/sci-biology/goby-1.9.7.3 new file mode 100644 index 000000000000..4ec2c92fab88 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-1.9.7.3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=>=virtual/jdk-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-libs/protobuf[java] dev-java/fastutil:5.0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 >=dev-java/java-config-2.2.0 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=A DNA sequencing data management framework +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +IUSE=+cpp elibc_FreeBSD elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=>=virtual/jre-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-libs/protobuf[java] dev-java/fastutil:5.0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 cpp? ( ~sci-biology/goby-cpp-1.9.7.3 ) >=dev-java/java-config-2.2.0 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-src.zip http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-deps.zip +_eclass_exported_funcs=pkg_preinst:java-pkg-2 pkg_setup:java-pkg-2 src_prepare:- src_configure:java-ant-2 src_compile:java-pkg-2 src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-2 b02dc1e46b3648e467b5fbdf7857cf28 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=8b122a674c7d130e120b6eb97c3bff77 diff --git a/metadata/md5-cache/sci-biology/goby-1.9.8.1 b/metadata/md5-cache/sci-biology/goby-1.9.8.1 new file mode 100644 index 000000000000..48312d9490c2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-1.9.8.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=>=virtual/jdk-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-libs/protobuf[java] dev-java/fastutil:5.0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 >=dev-java/java-config-2.2.0 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=A DNA sequencing data management framework +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +IUSE=+cpp elibc_FreeBSD elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=>=virtual/jre-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-libs/protobuf[java] dev-java/fastutil:5.0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 cpp? ( ~sci-biology/goby-cpp-1.9.8.1 ) >=dev-java/java-config-2.2.0 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-src.zip http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-deps.zip +_eclass_exported_funcs=pkg_preinst:java-pkg-2 pkg_setup:java-pkg-2 src_prepare:- src_configure:java-ant-2 src_compile:java-pkg-2 src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-2 b02dc1e46b3648e467b5fbdf7857cf28 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=cf94833e9cddf4257293422c8a1dd488 diff --git a/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 b/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 new file mode 100644 index 000000000000..a336f7ed25e6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=prepare +DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A DNA sequencing data management framework - C/C++ API +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-cpp.zip +_eclass_exported_funcs=src_prepare:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6524b71bf3ee0d73c02c9301388b3806 diff --git a/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 b/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 new file mode 100644 index 000000000000..28e2645b3913 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=prepare +DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A DNA sequencing data management framework - C/C++ API +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-cpp.zip +_eclass_exported_funcs=src_prepare:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=dd885c4ec853b595e8d09da5e5237c55 diff --git a/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 b/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 new file mode 100644 index 000000000000..22b44751ab7c --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A DNA sequencing data management framework - C/C++ API +EAPI=5 +HOMEPAGE=http://campagnelab.org/software/goby/ +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_2.0.1/goby_2.0.1-cpp.zip +_eclass_exported_funcs=src_prepare:- src_configure:autotools-utils src_compile:autotools-utils src_test:autotools-utils src_install:autotools-utils +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3119d3d694fd7478ab452660b5ae4d25 diff --git a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r1 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r1 new file mode 100644 index 000000000000..1c8ef2dc77c3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install test +DEPEND=pvm? ( sys-cluster/pvm ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=0 +HOMEPAGE=http://hmmer.janelia.org/ +IUSE=pvm threads +KEYWORDS=~alpha amd64 ia64 ~ppc ~sparc x86 +LICENSE=GPL-2 +RDEPEND=pvm? ( sys-cluster/pvm ) +SLOT=0 +SRC_URI=ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.tar.gz +_eclass_exported_funcs=src_compile:- src_test:- src_install:- +_md5_=2ab46ca98c65b05acb80ea06558e0d6e diff --git a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r2 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r2 new file mode 100644 index 000000000000..ad8b67d0f5bc --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install test +DEPEND=pvm? ( sys-cluster/pvm ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=0 +HOMEPAGE=http://hmmer.janelia.org/ +IUSE=pvm threads +KEYWORDS=~alpha amd64 ~ia64 ~ppc ppc64 ~sparc x86 +LICENSE=GPL-2 +RDEPEND=pvm? ( sys-cluster/pvm ) +SLOT=0 +SRC_URI=ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.tar.gz +_eclass_exported_funcs=src_compile:- src_test:- src_install:- +_md5_=facf72fb5eac940cd2a42cd5375b8887 diff --git a/metadata/md5-cache/sci-biology/hmmer-3.0 b/metadata/md5-cache/sci-biology/hmmer-3.0 new file mode 100644 index 000000000000..d620d0209169 --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-3.0 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare +DEPEND=mpi? ( virtual/mpi ) gsl? ( >=sci-libs/gsl-1.12 ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=4 +HOMEPAGE=http://hmmer.janelia.org/ +IUSE=+cpu_flags_x86_sse mpi +threads gsl static-libs +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) gsl? ( >=sci-libs/gsl-1.12 ) +SLOT=0 +SRC_URI=ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2cae24445997ef6c055ce2a697c2e91a diff --git a/metadata/md5-cache/sci-biology/iedera-1.04 b/metadata/md5-cache/sci-biology/iedera-1.04 new file mode 100644 index 000000000000..42a6cfb66d5e --- /dev/null +++ b/metadata/md5-cache/sci-biology/iedera-1.04 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=A subset seed design tool for DNA sequence alignment +EAPI=2 +HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.04.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=42417fbcf3312ce2e8bccbcb98b86e64 diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r1 b/metadata/md5-cache/sci-biology/iedera-1.05-r1 new file mode 100644 index 000000000000..f501415d2245 --- /dev/null +++ b/metadata/md5-cache/sci-biology/iedera-1.05-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A subset seed design tool for DNA sequence alignment +EAPI=6 +HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz +_eclass_exported_funcs=src_prepare:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=d1b6a914aed303aeffb28f45b2c79809 diff --git a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 new file mode 100644 index 000000000000..48102b3c2e73 --- /dev/null +++ b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Inference of RNA alignments +EAPI=4 +HOMEPAGE=http://infernal.janelia.org/ +IUSE=mpi +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) +SLOT=0 +SRC_URI=ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=34e807b33fc0c63f6787bf849c22463c diff --git a/metadata/md5-cache/sci-biology/iqpnni-3.2 b/metadata/md5-cache/sci-biology/iqpnni-3.2 new file mode 100644 index 000000000000..18e514079494 --- /dev/null +++ b/metadata/md5-cache/sci-biology/iqpnni-3.2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install +DESCRIPTION=Important Quartet Puzzling and NNI Operation +EAPI=0 +HOMEPAGE=http://www.cibiv.at/software/iqpnni/ +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.cibiv.at/software/iqpnni/iqpnni-3.2.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=4392358ea7f8e35440aa256a9c68f78f diff --git a/metadata/md5-cache/sci-biology/iqpnni-3.3.1 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+EAPI=4 +HOMEPAGE=http://www.cibiv.at/software/iqpnni/ +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.cibiv.at/software/iqpnni/iqpnni-3.3.2.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=f07584ffc4f24339d0a2c5757b926453 diff --git a/metadata/md5-cache/sci-biology/kalign-2.03 b/metadata/md5-cache/sci-biology/kalign-2.03 new file mode 100644 index 000000000000..0dc872cf042f --- /dev/null +++ b/metadata/md5-cache/sci-biology/kalign-2.03 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install unpack +DESCRIPTION=Global and progressive multiple sequence alignment +EAPI=0 +HOMEPAGE=http://msa.cgb.ki.se/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://debian/pool/main/k/kalign/kalign_2.03.orig.tar.gz +_eclass_exported_funcs=src_unpack:- src_install:- +_md5_=796265b19f9020a39acc88060b0a06dc diff --git a/metadata/md5-cache/sci-biology/kalign-2.03-r1 b/metadata/md5-cache/sci-biology/kalign-2.03-r1 new file mode 100644 index 000000000000..b8c911b90df1 --- /dev/null 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+LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://lagan.stanford.edu/lagan_web/lagan20.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=997a304caaa256e8cc911b8fe42218da diff --git a/metadata/md5-cache/sci-biology/lagan-2.0-r2 b/metadata/md5-cache/sci-biology/lagan-2.0-r2 new file mode 100644 index 000000000000..5c051a3b5bab --- /dev/null +++ b/metadata/md5-cache/sci-biology/lagan-2.0-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA +EAPI=2 +HOMEPAGE=http://lagan.stanford.edu/lagan_web/index.shtml +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://lagan.stanford.edu/lagan_web/lagan20.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 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dev-libs/libxml2:2 dev-libs/libxslt mpi? 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( virtual/mpi ) =dev-lang/python-2* +SLOT=0 +SRC_URI=http://meme.nbcr.net/downloads/meme_4.8.1.tar.gz +_eclass_exported_funcs=pkg_setup:python src_prepare:- src_configure:- src_test:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 python efc1c55fc44c5b7272fc2ffba73c3e6f toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3da487080e0d3a3f0051709b0f0c2cb5 diff --git a/metadata/md5-cache/sci-biology/mira-4.0.2 b/metadata/md5-cache/sci-biology/mira-4.0.2 new file mode 100644 index 000000000000..dd0647e4c003 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mira-4.0.2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install postinst prepare +DEPEND=dev-libs/boost[threads] dev-util/google-perftools <sys-devel/flex-2.6.0 app-editors/vim-core dev-libs/expat !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina +EAPI=5 +HOMEPAGE=http://www.chevreux.org/projects_mira.html +IUSE=doc +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x86-macos +LICENSE=GPL-2 +RDEPEND=dev-libs/boost[threads] dev-util/google-perftools +SLOT=0 +SRC_URI=http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/mira-4.0.2.tar.bz2 mirror://sourceforge/mira-assembler/mira_3rdparty_06-07-2012.tar.bz2 +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_configure:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=274ea72ac3aafd6c1b3dcc87329c1f5c diff --git a/metadata/md5-cache/sci-biology/mosaik-1.0.1367 b/metadata/md5-cache/sci-biology/mosaik-1.0.1367 new file mode 100644 index 000000000000..88de907c0407 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mosaik-1.0.1367 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install +DESCRIPTION=A reference-guided aligner for next-generation sequencing technologies +EAPI=2 +HOMEPAGE=https://code.google.com/p/mosaik-aligner/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://mosaik-aligner.googlecode.com/files/Mosaik-1.0.1367-source.tar.bz2 +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=93f61ecb2dc5485439047ba1c5c24da4 diff --git a/metadata/md5-cache/sci-biology/mosaik-1.0.1388 b/metadata/md5-cache/sci-biology/mosaik-1.0.1388 new file mode 100644 index 000000000000..c27d0c35bf14 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mosaik-1.0.1388 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=A reference-guided aligner for next-generation sequencing technologies +EAPI=2 +HOMEPAGE=https://code.google.com/p/mosaik-aligner/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://mosaik-aligner.googlecode.com/files/Mosaik-1.0.1388-source.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_md5_=2752545392ae0460b46c3d87cf951dc6 diff --git a/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 new file mode 100644 index 000000000000..ca61b047d6b9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=sci-biology/uchime mpi? ( virtual/mpi ) app-arch/unzip virtual/fortran +DESCRIPTION=A suite of algorithms for ecological bioinformatics +EAPI=5 +HOMEPAGE=http://www.mothur.org/ +IUSE=mpi +readline +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=sci-biology/uchime mpi? ( virtual/mpi ) virtual/fortran +SLOT=0 +SRC_URI=http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e fortran-2 8200fc942c3b3c1fc75d4d5bfd0ba7a2 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=b42407a0fafab0d97c3f25952ab2fdf8 diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 new file mode 100644 index 000000000000..f52bd2fe5e3c --- /dev/null +++ b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) +DESCRIPTION=Bayesian Inference of Phylogeny +EAPI=4 +HOMEPAGE=http://mrbayes.csit.fsu.edu/ +IUSE=debug mpi readline +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +RDEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) +SLOT=0 +SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=cbcfd648e8584c43dc080e4afca5f038 diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 new file mode 100644 index 000000000000..fc7d864d5729 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) +DESCRIPTION=Bayesian Inference of Phylogeny +EAPI=5 +HOMEPAGE=http://mrbayes.csit.fsu.edu/ +IUSE=debug mpi readline +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +RDEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) +SLOT=0 +SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=e9cc62e67d8723e0cb76bc19780862dd diff --git a/metadata/md5-cache/sci-biology/mummer-3.20 b/metadata/md5-cache/sci-biology/mummer-3.20 new file mode 100644 index 000000000000..735497412624 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mummer-3.20 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install unpack +DESCRIPTION=A rapid whole genome aligner +EAPI=0 +HOMEPAGE=http://mummer.sourceforge.net/ +IUSE=doc +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh +SLOT=0 +SRC_URI=mirror://sourceforge/mummer/MUMmer3.20.tar.gz +_eclass_exported_funcs=src_unpack:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=34bc41bb6f0e306a25a82485615b429d diff --git a/metadata/md5-cache/sci-biology/mummer-3.21 b/metadata/md5-cache/sci-biology/mummer-3.21 new file mode 100644 index 000000000000..ceecf3d7b2a7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mummer-3.21 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install unpack +DESCRIPTION=A rapid whole genome aligner +EAPI=0 +HOMEPAGE=http://mummer.sourceforge.net/ +IUSE=doc +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh +SLOT=0 +SRC_URI=mirror://sourceforge/mummer/MUMmer3.21.tar.gz +_eclass_exported_funcs=src_unpack:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=f7c3a4036f4bc40e941f2e0507d5e094 diff --git a/metadata/md5-cache/sci-biology/mummer-3.22-r1 b/metadata/md5-cache/sci-biology/mummer-3.22-r1 new file mode 100644 index 000000000000..587ce0233570 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mummer-3.22-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=A rapid whole genome aligner +EAPI=3 +HOMEPAGE=http://mummer.sourceforge.net/ +IUSE=doc +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh +SLOT=0 +SRC_URI=mirror://sourceforge/mummer/MUMmer3.22.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=442826d5952762aeb80a630690097f2d diff --git a/metadata/md5-cache/sci-biology/muscle-3.8.31 b/metadata/md5-cache/sci-biology/muscle-3.8.31 new file mode 100644 index 000000000000..1a1c6138a92f --- /dev/null +++ b/metadata/md5-cache/sci-biology/muscle-3.8.31 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Multiple sequence comparison by log-expectation +EAPI=5 +HOMEPAGE=http://www.drive5.com/muscle/ +KEYWORDS=amd64 ppc x86 +LICENSE=public-domain +RDEPEND=!sci-libs/libmuscle +SLOT=0 +SRC_URI=http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=66098426576b0d39431bfb0549bbeafd diff --git a/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 new file mode 100644 index 000000000000..9b8cae848bf2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) +DESCRIPTION=Development toolkit and applications for computational biology, including NCBI BLAST +EAPI=5 +HOMEPAGE=http://www.ncbi.nlm.nih.gov/ +IUSE=doc static-libs X +KEYWORDS=~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=public-domain +RDEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/ncbi.tar.gz -> ncbi-tools-2.2.26.tar.gz +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 prefix e7f2b9c6e57342e5d25eac22fce23062 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=18c39254e961f1799e6ad5e5408ed52e diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.3.0 b/metadata/md5-cache/sci-biology/newick-utils-1.3.0 new file mode 100644 index 000000000000..97c24ae3eab0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/newick-utils-1.3.0 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install test +DESCRIPTION=Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing) +EAPI=2 +HOMEPAGE=http://cegg.unige.ch/newick_utils +KEYWORDS=amd64 x86 +LICENSE=BSD +RDEPEND=!dev-games/libnw +SLOT=0 +SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.3.0.tar.gz +_eclass_exported_funcs=src_test:- src_install:- +_md5_=835a17d5f1779bde721ca3331061bdbc diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.5.0 b/metadata/md5-cache/sci-biology/newick-utils-1.5.0 new file mode 100644 index 000000000000..3142fd565f9c --- /dev/null +++ b/metadata/md5-cache/sci-biology/newick-utils-1.5.0 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install test +DESCRIPTION=Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing) +EAPI=2 +HOMEPAGE=http://cegg.unige.ch/newick_utils +KEYWORDS=~amd64 ~x86 +LICENSE=BSD +RDEPEND=!dev-games/libnw +SLOT=0 +SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.5.0.tar.gz +_eclass_exported_funcs=src_test:- src_install:- +_md5_=0917f326462c3f79b510c4ec5f051454 diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.6 b/metadata/md5-cache/sci-biology/newick-utils-1.6 new file mode 100644 index 000000000000..1a24cc167420 --- /dev/null +++ b/metadata/md5-cache/sci-biology/newick-utils-1.6 @@ -0,0 +1,11 @@ +DEFINED_PHASES=test +DESCRIPTION=Tools for processing phylogenetic trees +EAPI=6 +HOMEPAGE=http://cegg.unige.ch/newick_utils +KEYWORDS=~amd64 ~x86 +LICENSE=BSD +RDEPEND=!dev-games/libnw +SLOT=0 +SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.6.tar.gz +_eclass_exported_funcs=src_test:- +_md5_=c166f12c7d2afbfc81ed73a39ea35a1b diff --git a/metadata/md5-cache/sci-biology/njplot-2.3 b/metadata/md5-cache/sci-biology/njplot-2.3 new file mode 100644 index 000000000000..63df399377ca --- /dev/null +++ b/metadata/md5-cache/sci-biology/njplot-2.3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +DESCRIPTION=A phylogenetic tree drawing program which supports tree rooting +EAPI=2 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/njplot.html +KEYWORDS=amd64 x86 +LICENSE=public-domain +RDEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-2.3.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=1dedd3c07f1b65c208b003067cd68cf0 diff --git a/metadata/md5-cache/sci-biology/njplot-2.3-r1 b/metadata/md5-cache/sci-biology/njplot-2.3-r1 new file mode 100644 index 000000000000..c1d8a73316f5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/njplot-2.3-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +DESCRIPTION=A phylogenetic tree drawing program which supports tree rooting +EAPI=5 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/njplot.html +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-2.3.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=430ef4440179017c19c01eb71d3014f4 diff --git a/metadata/md5-cache/sci-biology/pals-1.0 b/metadata/md5-cache/sci-biology/pals-1.0 new file mode 100644 index 000000000000..704300f77cbe --- /dev/null +++ b/metadata/md5-cache/sci-biology/pals-1.0 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DESCRIPTION=Pairwise Aligner for Long Sequences +EAPI=2 +HOMEPAGE=http://www.drive5.com/pals/ +KEYWORDS=amd64 x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/pals-1.0.tar.gz +_eclass_exported_funcs=src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=e0ef21df5e1b1a15fd4532b3a9d6e6b7 diff --git a/metadata/md5-cache/sci-biology/paml-4.4c-r1 b/metadata/md5-cache/sci-biology/paml-4.4c-r1 new file mode 100644 index 000000000000..f47eb18844da --- /dev/null +++ b/metadata/md5-cache/sci-biology/paml-4.4c-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Phylogenetic Analysis by Maximum Likelihood +EAPI=5 +HOMEPAGE=http://abacus.gene.ucl.ac.uk/software/paml.html +KEYWORDS=amd64 x86 +LICENSE=free-noncomm +SLOT=0 +SRC_URI=http://abacus.gene.ucl.ac.uk/software/paml4.4c.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=a2299253a4624fe8430541631d399349 diff --git a/metadata/md5-cache/sci-biology/phrap-1.080812-r1 b/metadata/md5-cache/sci-biology/phrap-1.080812-r1 new file mode 100644 index 000000000000..f4d59712e6ec --- /dev/null +++ b/metadata/md5-cache/sci-biology/phrap-1.080812-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Shotgun assembly and alignment utilities +EAPI=5 +HOMEPAGE=http://www.phrap.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RDEPEND=dev-lang/perl dev-perl/Tk +RESTRICT=fetch +SLOT=0 +SRC_URI=phrap-1.080812-distrib.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_md5_=f826e1b40b9f0db523b295a5c6a899da diff --git a/metadata/md5-cache/sci-biology/phred-071220 b/metadata/md5-cache/sci-biology/phred-071220 new file mode 100644 index 000000000000..8f5ab0ac6e6f --- /dev/null +++ b/metadata/md5-cache/sci-biology/phred-071220 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DESCRIPTION=A base caller for Sanger DNA sequencing +EAPI=0 +HOMEPAGE=http://phrap.org/phredphrapconsed.html +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RESTRICT=fetch +SLOT=0 +SRC_URI=phred-dist-071220.b-acd.tar.gz +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=3fea319425324b49a3e8a1c1fc146efd diff --git a/metadata/md5-cache/sci-biology/phylip-3.69-r1 b/metadata/md5-cache/sci-biology/phylip-3.69-r1 new file mode 100644 index 000000000000..ac5a790f5cf8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.69-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw x11-proto/xproto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=freedist +RDEPEND=x11-libs/libXaw +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=fb82491d16d5f2daf7dbdac4f7a7003f diff --git a/metadata/md5-cache/sci-biology/phylip-3.696-r1 b/metadata/md5-cache/sci-biology/phylip-3.696-r1 new file mode 100644 index 000000000000..21c1b8968e0b --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.696-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw x11-proto/xproto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=BSD-2 +RDEPEND=x11-libs/libXaw +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=cbbb1bb5348a56ae12c42eca9a00d14e diff --git a/metadata/md5-cache/sci-biology/phyml-2.4.5-r2 b/metadata/md5-cache/sci-biology/phyml-2.4.5-r2 new file mode 100644 index 000000000000..372b6a12825a --- /dev/null +++ b/metadata/md5-cache/sci-biology/phyml-2.4.5-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Estimation of large phylogenies by maximum likelihood +EAPI=2 +HOMEPAGE=http://atgc.lirmm.fr/phyml/ +KEYWORDS=amd64 ppc x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.lirmm.fr/~guindon/phyml_v2.4.5.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6152894472e86fac62cd4a6e05ad553e diff --git a/metadata/md5-cache/sci-biology/picard-1.103 b/metadata/md5-cache/sci-biology/picard-1.103 new file mode 100644 index 000000000000..69da1e77b036 --- /dev/null +++ b/metadata/md5-cache/sci-biology/picard-1.103 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install preinst prepare setup test +DEPEND=>=virtual/jdk-1.6 dev-java/ant-apache-bcel:0 test? ( dev-java/testng:0 dev-lang/R ) dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0 source? ( app-arch/zip ) >=dev-java/ant-core-1.8.2:0 dev-java/ant-apache-bcel dev-java/testng:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=Java-based command-line utilities that manipulate SAM files +EAPI=5 +HOMEPAGE=http://picard.sourceforge.net/ +IUSE=elibc_FreeBSD doc source test elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=Apache-2.0 +RDEPEND=>=virtual/jre-1.6 dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0 source? ( app-arch/zip ) +SLOT=0 +SRC_URI=https://dev.gentoo.org/~ercpe/distfiles/sci-biology/picard/picard-1.103.tar.bz2 +_eclass_exported_funcs=pkg_preinst:java-pkg-2 pkg_setup:java-pkg-2 src_prepare:java-pkg-2 src_configure:java-ant-2 src_compile:java-pkg-2 src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e java-ant-2 7c5d0c274d390745f5033754a319f515 java-pkg-2 b02dc1e46b3648e467b5fbdf7857cf28 java-utils-2 4f0e83a2c108b9f3d74ecebf32e2f483 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=f33422ec9832c259cea81a18a74a8503 diff --git a/metadata/md5-cache/sci-biology/piler-1.0 b/metadata/md5-cache/sci-biology/piler-1.0 new file mode 100644 index 000000000000..2f4bc707ec13 --- /dev/null +++ b/metadata/md5-cache/sci-biology/piler-1.0 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Analysis of repetitive DNA found in genome sequences +EAPI=2 +HOMEPAGE=http://www.drive5.com/piler/ +KEYWORDS=amd64 x86 +LICENSE=public-domain +RDEPEND=|| ( sci-biology/muscle sci-libs/libmuscle ) sci-biology/pals +SLOT=0 +SRC_URI=mirror://gentoo/piler-1.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=21b4e96ca4b5ec6e0b82c8f783b16377 diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0 b/metadata/md5-cache/sci-biology/pilercr-1.0 new file mode 100644 index 000000000000..e4b6a94cbcb3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pilercr-1.0 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) +EAPI=4 +HOMEPAGE=http://www.drive5.com/pilercr/ +KEYWORDS=amd64 x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/pilercr-1.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=aa8c595d04f385296c2672be29f21d38 diff --git a/metadata/md5-cache/sci-biology/plink-1.07-r1 b/metadata/md5-cache/sci-biology/plink-1.07-r1 new file mode 100644 index 000000000000..e34cd78ef3db --- /dev/null +++ b/metadata/md5-cache/sci-biology/plink-1.07-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare +DEPEND=app-arch/unzip lapack? ( virtual/pkgconfig ) +DESCRIPTION=Whole genome association analysis toolset +EAPI=4 +HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ +IUSE=lapack -webcheck R +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib lapack? ( virtual/lapack ) +SLOT=0 +SRC_URI=http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=1514de2a10550eec3709c846e4e3f075 diff --git a/metadata/md5-cache/sci-biology/plink-1.90_pre140514 b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 new file mode 100644 index 000000000000..5f1d503483c9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=app-arch/unzip virtual/pkgconfig +DESCRIPTION=Whole genome association analysis toolset +EAPI=5 +HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib virtual/cblas virtual/lapack +SLOT=0 +SRC_URI=http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> plink-1.90_pre140514.zip +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=0bc8bcce219140bdc4ef2672a457932a diff --git a/metadata/md5-cache/sci-biology/poa-2-r1 b/metadata/md5-cache/sci-biology/poa-2-r1 new file mode 100644 index 000000000000..b773b5b50ac7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/poa-2-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Fast multiple sequence alignments using partial-order graphs +EAPI=5 +HOMEPAGE=http://bioinfo.mbi.ucla.edu/poa/ +IUSE=static-libs +KEYWORDS=~x86 ~amd64 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/poamsa/poaV2.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=c694b3bde674902a9601f856356cf311 diff --git a/metadata/md5-cache/sci-biology/prank-100701 b/metadata/md5-cache/sci-biology/prank-100701 new file mode 100644 index 000000000000..6eaf7ca17a8b --- /dev/null +++ b/metadata/md5-cache/sci-biology/prank-100701 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Probabilistic Alignment Kit +EAPI=4 +HOMEPAGE=http://wasabiapp.org/software/prank/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100701.tgz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=99862c8618b27fc12eab5d6cb0c23ae6 diff --git a/metadata/md5-cache/sci-biology/prank-111130 b/metadata/md5-cache/sci-biology/prank-111130 new file mode 100644 index 000000000000..7adb62060e06 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prank-111130 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Probabilistic Alignment Kit +EAPI=4 +HOMEPAGE=http://wasabiapp.org/software/prank/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=https://prank-msa.googlecode.com/files/prank.src.111130.tgz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=bd13e7f3e9d7aaabf98c6d09eef515de diff --git a/metadata/md5-cache/sci-biology/prank-140603 b/metadata/md5-cache/sci-biology/prank-140603 new file mode 100644 index 000000000000..144dcec9645e --- /dev/null +++ b/metadata/md5-cache/sci-biology/prank-140603 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Probabilistic Alignment Kit +EAPI=4 +HOMEPAGE=http://wasabiapp.org/software/prank/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=a78b8fe781e96a7748fe5d249d518725 diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.5 b/metadata/md5-cache/sci-biology/primer3-2.3.5 new file mode 100644 index 000000000000..c7ed1167d352 --- /dev/null +++ b/metadata/md5-cache/sci-biology/primer3-2.3.5 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=dev-lang/perl +DESCRIPTION=Primer Design for PCR reactions +EAPI=5 +HOMEPAGE=http://primer3.sourceforge.net/ +KEYWORDS=amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/primer3/2.3.5/primer3-2.3.5.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=89df84d198ccabc6e171bd151b0d86e4 diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.6 b/metadata/md5-cache/sci-biology/primer3-2.3.6 new file mode 100644 index 000000000000..c3e2e82d93d7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/primer3-2.3.6 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=dev-lang/perl +DESCRIPTION=Primer Design for PCR reactions +EAPI=5 +HOMEPAGE=http://primer3.sourceforge.net/ +KEYWORDS=amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/primer3/2.3.6/primer3-src-2.3.6.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=fbc5952f543d327fcb6b99cf43241909 diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.7 b/metadata/md5-cache/sci-biology/primer3-2.3.7 new file mode 100644 index 000000000000..9ceee419017f --- /dev/null +++ b/metadata/md5-cache/sci-biology/primer3-2.3.7 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=dev-lang/perl +DESCRIPTION=Primer Design for PCR reactions +EAPI=6 +HOMEPAGE=http://primer3.sourceforge.net/ +KEYWORDS=~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/project/primer3/primer3/2.3.7/primer3-2.3.7.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2d22589e3f0ecb3ac49bc9fde62ab1f2 diff --git a/metadata/md5-cache/sci-biology/prints-39.0 b/metadata/md5-cache/sci-biology/prints-39.0 new file mode 100644 index 000000000000..584a2da6793f --- /dev/null +++ b/metadata/md5-cache/sci-biology/prints-39.0 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A protein motif fingerprint database +EAPI=0 +HOMEPAGE=http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ +IUSE=emboss minimal +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/prints-39.0.tar.bz2 +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=92901e212ac7746e9ff9c941a1cdae10 diff --git a/metadata/md5-cache/sci-biology/probcons-1.12-r1 b/metadata/md5-cache/sci-biology/probcons-1.12-r1 new file mode 100644 index 000000000000..f2b01ef6ba43 --- /dev/null +++ b/metadata/md5-cache/sci-biology/probcons-1.12-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences +EAPI=5 +HOMEPAGE=http://probcons.stanford.edu/ +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=!sci-geosciences/gmt sci-visualization/gnuplot +SLOT=0 +SRC_URI=http://probcons.stanford.edu/probcons_v1_12.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=7832c26904cb58b1ed5527c9b9cae1c8 diff --git a/metadata/md5-cache/sci-biology/prodigal-2.50 b/metadata/md5-cache/sci-biology/prodigal-2.50 new file mode 100644 index 000000000000..ce8bbe1d75c1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prodigal-2.50 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm +EAPI=2 +HOMEPAGE=http://prodigal.ornl.gov/ https://code.google.com/p/prodigal/ +KEYWORDS=~amd64 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=https://prodigal.googlecode.com/files/prodigal.v2_50.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_md5_=b80d634fc8ec98c4e1eb79b45e62ab1e diff --git a/metadata/md5-cache/sci-biology/prodigal-2.60 b/metadata/md5-cache/sci-biology/prodigal-2.60 new file mode 100644 index 000000000000..f2c5b6ff9b1e --- /dev/null +++ b/metadata/md5-cache/sci-biology/prodigal-2.60 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm +EAPI=2 +HOMEPAGE=http://prodigal.ornl.gov/ https://code.google.com/p/prodigal/ +KEYWORDS=~amd64 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=https://prodigal.googlecode.com/files/prodigal.v2_60.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_md5_=305999f17f2c525994f97ab8a7636ff9 diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.39 b/metadata/md5-cache/sci-biology/profphd-1.0.39 new file mode 100644 index 000000000000..bd96c4bf3b24 --- /dev/null +++ b/metadata/md5-cache/sci-biology/profphd-1.0.39 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=dev-lang/perl +DESCRIPTION=Secondary structure and solvent accessibility predictor +EAPI=5 +HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils +SLOT=0 +SRC_URI=ftp://rostlab.org/profphd/profphd-1.0.39.tar.xz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=d6903679ef8eac2c123c4556ef80c8ec diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.40 b/metadata/md5-cache/sci-biology/profphd-1.0.40 new file mode 100644 index 000000000000..6bb3dd8109f6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/profphd-1.0.40 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=dev-lang/perl +DESCRIPTION=Secondary structure and solvent accessibility predictor +EAPI=5 +HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils +SLOT=0 +SRC_URI=ftp://rostlab.org/profphd/profphd-1.0.40.tar.xz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=5278fe0b86d8b4447a0f4492214757a0 diff --git a/metadata/md5-cache/sci-biology/prosite-19.36 b/metadata/md5-cache/sci-biology/prosite-19.36 new file mode 100644 index 000000000000..ce30d7d2427d --- /dev/null +++ b/metadata/md5-cache/sci-biology/prosite-19.36 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A protein families and domains database +EAPI=0 +HOMEPAGE=http://ca.expasy.org/prosite +IUSE=emboss minimal +KEYWORDS=amd64 ppc x86 +LICENSE=swiss-prot +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/prosite-19.36.tar.bz2 +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=add1e735422c0eb765c798ffa290416f diff --git a/metadata/md5-cache/sci-biology/prosite-20.36 b/metadata/md5-cache/sci-biology/prosite-20.36 new file mode 100644 index 000000000000..6b5b127917d1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prosite-20.36 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A protein families and domains database +EAPI=0 +HOMEPAGE=http://ca.expasy.org/prosite +IUSE=emboss minimal +KEYWORDS=amd64 ~ppc x86 +LICENSE=swiss-prot +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/prosite-20.36.tar.bz2 +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=219e62658f07a2f2ca280e4efbde8c9e diff --git a/metadata/md5-cache/sci-biology/prosite-20.52 b/metadata/md5-cache/sci-biology/prosite-20.52 new file mode 100644 index 000000000000..ebfe77289fa8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prosite-20.52 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A protein families and domains database +EAPI=0 +HOMEPAGE=http://ca.expasy.org/prosite +IUSE=emboss minimal +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=swiss-prot +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/prosite-20.52.tar.bz2 +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=99cc1069ef5cf28badb48f55a0ca904a diff --git a/metadata/md5-cache/sci-biology/prosite-20.72 b/metadata/md5-cache/sci-biology/prosite-20.72 new file mode 100644 index 000000000000..c490259ab077 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prosite-20.72 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A protein families and domains database +EAPI=0 +HOMEPAGE=http://ca.expasy.org/prosite +IUSE=emboss minimal +KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=swiss-prot +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/prosite-20.72.tar.bz2 +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=6b7103738cf6b7c7db1f30a81ec09132 diff --git a/metadata/md5-cache/sci-biology/psipred-3.1 b/metadata/md5-cache/sci-biology/psipred-3.1 new file mode 100644 index 000000000000..6f496a8df0d8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=3 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred31.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 prefix e7f2b9c6e57342e5d25eac22fce23062 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=059ee957489f4c11d1c0946924cb3a7f diff --git a/metadata/md5-cache/sci-biology/psipred-3.2 b/metadata/md5-cache/sci-biology/psipred-3.2 new file mode 100644 index 000000000000..4b2d9a88ee9e --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=3 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred32.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 prefix e7f2b9c6e57342e5d25eac22fce23062 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=3048d78763d0d830803b3252e9728250 diff --git a/metadata/md5-cache/sci-biology/psipred-3.2.1 b/metadata/md5-cache/sci-biology/psipred-3.2.1 new file mode 100644 index 000000000000..f4c89b3c8ccf --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.2.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=4 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred321.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 prefix e7f2b9c6e57342e5d25eac22fce23062 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=2ad13218bde0c6cf5a5ab5caee939086 diff --git a/metadata/md5-cache/sci-biology/psipred-3.3 b/metadata/md5-cache/sci-biology/psipred-3.3 new file mode 100644 index 000000000000..10a203106b49 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=4 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.3.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 prefix e7f2b9c6e57342e5d25eac22fce23062 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=369220ea4bf38d546a107d8503320973 diff --git a/metadata/md5-cache/sci-biology/psipred-3.4 b/metadata/md5-cache/sci-biology/psipred-3.4 new file mode 100644 index 000000000000..84a79f83e413 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=5 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=app-shells/tcsh sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.4.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 prefix e7f2b9c6e57342e5d25eac22fce23062 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=8cae719195a0bc1655657fc75a690b0f diff --git a/metadata/md5-cache/sci-biology/psipred-3.5 b/metadata/md5-cache/sci-biology/psipred-3.5 new file mode 100644 index 000000000000..98522ab2d0f8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.5 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=5 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=app-shells/tcsh sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.5.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 prefix e7f2b9c6e57342e5d25eac22fce23062 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=8cae719195a0bc1655657fc75a690b0f diff --git a/metadata/md5-cache/sci-biology/pysam-0.9.0 b/metadata/md5-cache/sci-biology/pysam-0.9.0 new file mode 100644 index 000000000000..59e013434316 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pysam-0.9.0 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND==sci-libs/htslib-1.3* dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format +EAPI=6 +HOMEPAGE=https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam +IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND==sci-libs/htslib-1.3* python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 ) +SLOT=0 +SRC_URI=https://github.com/pysam-developers/pysam/archive/v0.9.0.tar.gz -> pysam-0.9.0.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:distutils-r1 src_compile:- src_test:distutils-r1 src_install:distutils-r1 +_eclasses_=distutils-r1 4e8ac1ba76ddacd8f7c0289aa586a34c multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=4347b0e64a8de2968bb9d80fc701d2ea diff --git a/metadata/md5-cache/sci-biology/qrna-2.0.3c-r1 b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r1 new file mode 100644 index 000000000000..6e57f773c506 --- /dev/null +++ b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=dev-lang/perl sci-biology/hmmer +DESCRIPTION=Prototype ncRNA genefinder +EAPI=4 +HOMEPAGE=http://selab.janelia.org/software.html +KEYWORDS=amd64 ~ppc x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl sci-biology/hmmer +SLOT=0 +SRC_URI=mirror://gentoo/qrna-2.0.3c.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=a604c43b2c62327815727613b2748c6f diff --git a/metadata/md5-cache/sci-biology/raxml-7.2.6 b/metadata/md5-cache/sci-biology/raxml-7.2.6 new file mode 100644 index 000000000000..24d3ea94ce19 --- /dev/null +++ b/metadata/md5-cache/sci-biology/raxml-7.2.6 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees +EAPI=5 +HOMEPAGE=http://wwwkramer.in.tum.de/exelixis/software.html +IUSE=cpu_flags_x86_sse3 +threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +REQUIRED_USE=cpu_flags_x86_sse3 +SLOT=0 +SRC_URI=http://wwwkramer.in.tum.de/exelixis/software/RAxML-7.2.6.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6ce26877e006d2d080de7e0b2d55a7b7 diff --git a/metadata/md5-cache/sci-biology/rebase-1601 b/metadata/md5-cache/sci-biology/rebase-1601 new file mode 100644 index 000000000000..c0c212b25eb6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1601 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=5 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1601.tar.xz +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=b1d41ea0939d982d726f7f26c96abe1f diff --git a/metadata/md5-cache/sci-biology/rebase-1602 b/metadata/md5-cache/sci-biology/rebase-1602 new file mode 100644 index 000000000000..c7649d00a365 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1602 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=5 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1602.tar.xz +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=b1d41ea0939d982d726f7f26c96abe1f diff --git a/metadata/md5-cache/sci-biology/rebase-1604 b/metadata/md5-cache/sci-biology/rebase-1604 new file mode 100644 index 000000000000..30e11feef9a2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1604 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=5 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1604.tar.xz +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=316c807c873c162f55b6a3e40715040b diff --git a/metadata/md5-cache/sci-biology/recon-1.06-r1 b/metadata/md5-cache/sci-biology/recon-1.06-r1 new file mode 100644 index 000000000000..27986e1ad80f --- /dev/null +++ b/metadata/md5-cache/sci-biology/recon-1.06-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Automated de novo identification of repeat families from genomic sequences +EAPI=4 +HOMEPAGE=http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html +IUSE=examples +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.repeatmasker.org/RECON1.06.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=5dc463aa504ef23ac98031de21caed4e diff --git a/metadata/md5-cache/sci-biology/recon-1.06-r2 b/metadata/md5-cache/sci-biology/recon-1.06-r2 new file mode 100644 index 000000000000..0fdeb11ce6d6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/recon-1.06-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Automated de novo identification of repeat families from genomic sequences +EAPI=4 +HOMEPAGE=http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html +IUSE=examples +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.repeatmasker.org/RECON1.06.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3e653eec95c5d1dbd63cd1cdc1e98b06 diff --git a/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 b/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 new file mode 100644 index 000000000000..5373c480b08e --- /dev/null +++ b/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Screen DNA sequences for interspersed repeats and low complexity DNA +EAPI=5 +HOMEPAGE=http://repeatmasker.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=OSL-2.1 +RDEPEND=sci-biology/rmblast sci-biology/trf sci-biology/repeatmasker-libraries +SLOT=0 +SRC_URI=http://www.repeatmasker.org/RepeatMasker-open-4-0-1.tar.gz +_eclass_exported_funcs=src_configure:- src_install:- +_md5_=b28fa4d66bb5be71f31642c296093d11 diff --git a/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 b/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 new file mode 100644 index 000000000000..995e2041f3bf --- /dev/null +++ b/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install +DESCRIPTION=A special version of RepBase used by RepeatMasker +EAPI=5 +HOMEPAGE=http://repeatmasker.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=all-rights-reserved +RESTRICT=fetch +SLOT=0 +SRC_URI=repeatmaskerlibraries-20120418.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=b4d050c303955f9f4d69a65b4f42b2ad diff --git a/metadata/md5-cache/sci-biology/rmblast-1.2-r1 b/metadata/md5-cache/sci-biology/rmblast-1.2-r1 new file mode 100644 index 000000000000..f5a3b82b062a --- /dev/null +++ b/metadata/md5-cache/sci-biology/rmblast-1.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare +DEPEND=dev-libs/boost app-arch/cpio +DESCRIPTION=RepeatMasker compatible version of NCBI BLAST+ +EAPI=5 +HOMEPAGE=http://www.repeatmasker.org/RMBlast.html +KEYWORDS=~amd64 ~x86 +LICENSE=OSL-2.1 +RDEPEND=dev-libs/boost +SLOT=0 +SRC_URI=http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=4c288235ce00754a3b76fa3068a818b2 diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713 b/metadata/md5-cache/sci-biology/rnaview-20040713 new file mode 100644 index 000000000000..cb0614ef9641 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rnaview-20040713 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install unpack +DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +EAPI=0 +HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html +KEYWORDS=~amd64 x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 +_eclass_exported_funcs=src_unpack:- src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=fe3a0b850dcdb0fcd3c4b8ff9be47b48 diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r2 b/metadata/md5-cache/sci-biology/rnaview-20040713-r2 new file mode 100644 index 000000000000..390498944add --- /dev/null +++ b/metadata/md5-cache/sci-biology/rnaview-20040713-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +EAPI=2 +HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=22ccaa60a98821105bd95c1f49baf5d0 diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r3 b/metadata/md5-cache/sci-biology/rnaview-20040713-r3 new file mode 100644 index 000000000000..6eeeb8392d8f --- /dev/null +++ b/metadata/md5-cache/sci-biology/rnaview-20040713-r3 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +EAPI=4 +HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=e7277ead215a53f06aa591bc3dcea8a1 diff --git a/metadata/md5-cache/sci-biology/samtools-0.1.12 b/metadata/md5-cache/sci-biology/samtools-0.1.12 new file mode 100644 index 000000000000..df30836b80a4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-0.1.12 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=2 +HOMEPAGE=http://samtools.sourceforge.net/ +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=MIT +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-0.1.12a.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_install:- +_md5_=dbd13692bde5f1bc8aca3971e257d35e diff --git a/metadata/md5-cache/sci-biology/samtools-0.1.19-r2 b/metadata/md5-cache/sci-biology/samtools-0.1.19-r2 new file mode 100644 index 000000000000..1d8b7055db9c --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-0.1.19-r2 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses:0= virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=5 +HOMEPAGE=http://samtools.sourceforge.net/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=sys-libs/ncurses:0= dev-lang/lua dev-lang/perl +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-0.1.19.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=386582eb3ff9435a92dd20bdbd248cbc diff --git a/metadata/md5-cache/sci-biology/samtools-0.1.20-r2 b/metadata/md5-cache/sci-biology/samtools-0.1.20-r2 new file mode 100644 index 000000000000..efaf76499dd3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-0.1.20-r2 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install postinst prepare +DEPEND=sys-libs/ncurses:0= dev-lang/perl virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=6 +HOMEPAGE=http://samtools.sourceforge.net/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=sys-libs/ncurses:0= dev-lang/perl +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0.1-legacy +SRC_URI=https://github.com/samtools/samtools/archive/0.1.20.tar.gz -> samtools-0.1.20.tar.gz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=9e04100e7a9246f6b77261416f9c77c4 diff --git a/metadata/md5-cache/sci-biology/samtools-1.0 b/metadata/md5-cache/sci-biology/samtools-1.0 new file mode 100644 index 000000000000..8c30f003d4fa --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.0 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses:0= sci-libs/htslib virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=5 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=sys-libs/ncurses:0= sci-libs/htslib dev-lang/lua dev-lang/perl +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.0.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=db99b61f10fd031a95c3ba948438e007 diff --git a/metadata/md5-cache/sci-biology/samtools-1.0-r1 b/metadata/md5-cache/sci-biology/samtools-1.0-r1 new file mode 100644 index 000000000000..5cdb27d4e1d8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.0-r1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses:0= sci-libs/htslib virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=5 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples python_targets_python2_7 +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=sys-libs/ncurses:0= sci-libs/htslib dev-lang/lua dev-lang/perl +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.0.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=cf94159379e0b14da650368a72d518dd diff --git a/metadata/md5-cache/sci-biology/samtools-1.1 b/metadata/md5-cache/sci-biology/samtools-1.1 new file mode 100644 index 000000000000..dfafe318f30f --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=sys-libs/ncurses:0= ~sci-libs/htslib-1.1 virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=5 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=sys-libs/ncurses:0= ~sci-libs/htslib-1.1 dev-lang/lua dev-lang/perl +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.1.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=9233bca436af5041a19d8326e816d011 diff --git a/metadata/md5-cache/sci-biology/samtools-1.2 b/metadata/md5-cache/sci-biology/samtools-1.2 new file mode 100644 index 000000000000..e2fac57f5cda --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.2 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=sys-libs/ncurses:0= >=sci-libs/htslib-1.2 virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=5 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=sys-libs/ncurses:0= >=sci-libs/htslib-1.2 dev-lang/lua dev-lang/perl +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.2.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=75d7314287663a3f5ea5b17060bd2081 diff --git a/metadata/md5-cache/sci-biology/samtools-1.3-r1 b/metadata/md5-cache/sci-biology/samtools-1.3-r1 new file mode 100644 index 000000000000..defd5fa009eb --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.3-r1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=sys-libs/ncurses:0= =sci-libs/htslib-1.3* dev-lang/perl virtual/pkgconfig !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=6 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=sys-libs/ncurses:0= =sci-libs/htslib-1.3* dev-lang/perl +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.3.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c libtool 4890219c51da247200223277f993e054 multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=bf4d95b9d61aabecfc5d1eb4039ebc7d diff --git a/metadata/md5-cache/sci-biology/seaview-4.3.5 b/metadata/md5-cache/sci-biology/seaview-4.3.5 new file mode 100644 index 000000000000..842347bb84d9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.3.5 @@ -0,0 +1,14 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=5 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=amd64 ppc x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.3.5.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=9d788d989511d355673d31e81a3f34e8 diff --git a/metadata/md5-cache/sci-biology/seaview-4.5.4 b/metadata/md5-cache/sci-biology/seaview-4.5.4 new file mode 100644 index 000000000000..ffc1acc77ffe --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.5.4 @@ -0,0 +1,14 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=5 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=amd64 ppc x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.5.4.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6226d6428885158b7d6d73e153e2ae2f diff --git a/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 new file mode 100644 index 000000000000..436f5d463f0b --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install postinst prepare setup test +DEPEND=sys-libs/zlib app-arch/bzip2 test? ( dev-python/nose[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),python_single_target_python2_7(+)] ) sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 test python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +REQUIRED_USE=python_targets_python2_7 cpu_flags_x86_sse4_1 +SLOT=1.4 +SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-1.4.2.tar.gz +_eclass_exported_funcs=pkg_postinst:- pkg_setup:python-single-r1 src_prepare:- src_configure:- src_compile:cmake-utils src_test:cmake-utils src_install:- +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 python-single-r1 2ebea8fbab356d63110245129a67a6dd python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=33a44ba69cb29b108cba8aebccd91632 diff --git a/metadata/md5-cache/sci-biology/seqan-2.1.1 b/metadata/md5-cache/sci-biology/seqan-2.1.1 new file mode 100644 index 000000000000..f17b455b3f76 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-2.1.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare setup test +DEPEND=sys-libs/zlib app-arch/bzip2 doc? ( dev-python/sphinx[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),python_single_target_python2_7(+)] ) test? ( dev-python/nose[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),python_single_target_python2_7(+)] ) sys-devel/make >=dev-util/cmake-2.8.12 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 doc test python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +REQUIRED_USE=python_targets_python2_7 cpu_flags_x86_sse4_1 +SLOT=2.1 +SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-2.1.1.tar.gz +_eclass_exported_funcs=pkg_setup:python-single-r1 src_prepare:- src_configure:- src_compile:- src_test:cmake-utils src_install:- +_eclasses_=cmake-utils 422bbd1bee2557490177a34dbe0a662b eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 python-single-r1 2ebea8fbab356d63110245129a67a6dd python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=2415e0c180b4739d2eb92f3ee7789206 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.0.1 b/metadata/md5-cache/sci-biology/shrimp-2.0.1 new file mode 100644 index 000000000000..8225e1282064 --- /dev/null +++ b/metadata/md5-cache/sci-biology/shrimp-2.0.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs +DESCRIPTION=SHort Read Mapping Package +EAPI=4 +HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ +IUSE=custom-cflags +KEYWORDS=amd64 x86 +LICENSE=shrimp +RDEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs +SLOT=0 +SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_0_1.src.tar.gz +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=ca9f79b1dc8cc6c457969f3bfc6dad48 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.2.3 b/metadata/md5-cache/sci-biology/shrimp-2.2.3 new file mode 100644 index 000000000000..512115ecb60a --- /dev/null +++ b/metadata/md5-cache/sci-biology/shrimp-2.2.3 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install prepare pretend setup +DEPEND=!sci-mathematics/cado-nfs +DESCRIPTION=SHort Read Mapping Package +EAPI=5 +HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ +IUSE=custom-cflags +cpu_flags_x86_sse2 python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=shrimp +RDEPEND=!sci-mathematics/cado-nfs >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),python_single_target_python2_7(+)] +REQUIRED_USE=python_targets_python2_7 +SLOT=0 +SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_2_3.src.tar.gz +_eclass_exported_funcs=pkg_pretend:- pkg_setup:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 python-single-r1 2ebea8fbab356d63110245129a67a6dd python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=4f8021ced803372cddeb27e1a3b6521c diff --git a/metadata/md5-cache/sci-biology/sibsim4-0.20 b/metadata/md5-cache/sci-biology/sibsim4-0.20 new file mode 100644 index 000000000000..4016001054a7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sibsim4-0.20 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=A rewrite and improvement upon sim4, a DNA-mRNA aligner +EAPI=5 +HOMEPAGE=http://sibsim4.sourceforge.net/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/sibsim4/SIBsim4-0.20.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=9df129026fb913d20a07f5dd4658f408 diff --git a/metadata/md5-cache/sci-biology/sim4-20030921 b/metadata/md5-cache/sci-biology/sim4-20030921 new file mode 100644 index 000000000000..1b5199a3668b --- /dev/null +++ b/metadata/md5-cache/sci-biology/sim4-20030921 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=A program to align cDNA and genomic DNA +EAPI=0 +HOMEPAGE=http://globin.cse.psu.edu/html/docs/sim4.html +KEYWORDS=x86 ~ppc +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=1f9553f10941eb2db6ae6c98bda33f30 diff --git a/metadata/md5-cache/sci-biology/sim4-20030921-r1 b/metadata/md5-cache/sci-biology/sim4-20030921-r1 new file mode 100644 index 000000000000..9cd3f2d21778 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sim4-20030921-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DESCRIPTION=A program to align cDNA and genomic DNA +EAPI=0 +HOMEPAGE=http://globin.cse.psu.edu/html/docs/sim4.html +KEYWORDS=~amd64 ~ppc ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz +_eclass_exported_funcs=src_compile:- src_install:- +_eclasses_=multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=e1e0b2ce50bc94c54d2fb0ef73b85af3 diff --git a/metadata/md5-cache/sci-biology/snpfile-2.0.1 b/metadata/md5-cache/sci-biology/snpfile-2.0.1 new file mode 100644 index 000000000000..1de71522cac8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/snpfile-2.0.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=dev-libs/boost +DESCRIPTION=A library and API for manipulating large SNP datasets +EAPI=2 +HOMEPAGE=http://www.birc.au.dk/~mailund/SNPFile/ +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=dev-libs/boost +SLOT=0 +SRC_URI=http://www.birc.au.dk/~mailund/SNPFile/download/snpfile-2.0.1.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=7fec83257ef5001d9827b0326638df67 diff --git a/metadata/md5-cache/sci-biology/snpfile-2.0.1-r1 b/metadata/md5-cache/sci-biology/snpfile-2.0.1-r1 new file mode 100644 index 000000000000..798dd836b942 --- /dev/null +++ b/metadata/md5-cache/sci-biology/snpfile-2.0.1-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/boost !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A library and API for manipulating large SNP datasets +EAPI=4 +HOMEPAGE=http://www.birc.au.dk/~mailund/SNPFile/ +IUSE=static-libs +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=dev-libs/boost +SLOT=0 +SRC_URI=http://www.birc.au.dk/~mailund/SNPFile/download/snpfile-2.0.1.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=18767f7f8f9a5ca8d5256c034b152bb7 diff --git a/metadata/md5-cache/sci-biology/stride-20011129-r1 b/metadata/md5-cache/sci-biology/stride-20011129-r1 new file mode 100644 index 000000000000..7b61b8440fb8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/stride-20011129-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Protein secondary structure assignment from atomic coordinates +EAPI=5 +HOMEPAGE=http://webclu.bio.wzw.tum.de/stride/ +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos +LICENSE=STRIDE +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/stride.tar.gz https://dev.gentoo.org/~jlec/distfiles/stride-20060723-update.patch.bz2 +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=01b4d26980038bd00786a70c9cd79963 diff --git a/metadata/md5-cache/sci-biology/t-coffee-11.00-r1 b/metadata/md5-cache/sci-biology/t-coffee-11.00-r1 new file mode 100644 index 000000000000..6c071cae7b25 --- /dev/null +++ b/metadata/md5-cache/sci-biology/t-coffee-11.00-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=A multiple sequence alignment package +EAPI=5 +HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html +IUSE=examples +KEYWORDS=~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=sci-biology/clustalw sci-chemistry/tm-align +SLOT=0 +SRC_URI=http://www.tcoffee.org/Packages/Stable/Version_11.00.8cbe486/T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=f6ad616b3dcf58a2f7c0551f7aea38a6 diff --git a/metadata/md5-cache/sci-biology/t-coffee-9.03.1318-r1 b/metadata/md5-cache/sci-biology/t-coffee-9.03.1318-r1 new file mode 100644 index 000000000000..b6c1fc37e07a --- /dev/null +++ b/metadata/md5-cache/sci-biology/t-coffee-9.03.1318-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=virtual/fortran +DESCRIPTION=A multiple sequence alignment package +EAPI=5 +HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html +IUSE=examples +KEYWORDS=amd64 ppc ~ppc64 x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=sci-biology/clustalw sci-chemistry/tm-align virtual/fortran +SLOT=0 +SRC_URI=http://www.tcoffee.org/Packages/Stable/Version_9.03.r1318/T-COFFEE_distribution_Version_9.03.r1318.tar.gz +_eclass_exported_funcs=pkg_setup:fortran-2 src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e fortran-2 8200fc942c3b3c1fc75d4d5bfd0ba7a2 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=d6f0c1f80bcc0790b5e24d8e96f831bb diff --git a/metadata/md5-cache/sci-biology/tophat-1.0.12 b/metadata/md5-cache/sci-biology/tophat-1.0.12 new file mode 100644 index 000000000000..fd72b24f28cd --- /dev/null +++ b/metadata/md5-cache/sci-biology/tophat-1.0.12 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=!<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A fast splice junction mapper for RNA-Seq reads +EAPI=2 +HOMEPAGE=http://tophat.cbcb.umd.edu/ +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=sci-biology/bowtie +SLOT=0 +SRC_URI=http://tophat.cbcb.umd.edu/downloads/tophat-1.0.12.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=e77d3500a52473f554abdde6a1d91b6c diff --git a/metadata/md5-cache/sci-biology/tophat-2.1.1 b/metadata/md5-cache/sci-biology/tophat-2.1.1 new file mode 100644 index 000000000000..afd8b523be03 --- /dev/null +++ b/metadata/md5-cache/sci-biology/tophat-2.1.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install postinst prepare setup +DEPEND=dev-libs/boost sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 sci-biology/seqan:1.4 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Python-based splice junction mapper for RNA-Seq reads using bowtie2 +EAPI=6 +HOMEPAGE=https://ccb.jhu.edu/software/tophat/ +IUSE=debug python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=dev-libs/boost sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 +SLOT=0 +SRC_URI=https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz +_eclass_exported_funcs=pkg_postinst:- pkg_setup:python-single-r1 src_prepare:- src_configure:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 python-single-r1 2ebea8fbab356d63110245129a67a6dd python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=99a8a65bd99f7819e12ab99f02b47509 diff --git a/metadata/md5-cache/sci-biology/transfac-3.2 b/metadata/md5-cache/sci-biology/transfac-3.2 new file mode 100644 index 000000000000..442a4718d53f --- /dev/null +++ b/metadata/md5-cache/sci-biology/transfac-3.2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A database of eucaryotic transcription factors +EAPI=0 +HOMEPAGE=http://www.gene-regulation.com/pub/databases.html +IUSE=emboss minimal +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=3 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z +_eclass_exported_funcs=src_compile:- src_install:- +_md5_=39ef300168197d20ec49bae89abf1904 diff --git a/metadata/md5-cache/sci-biology/tree-puzzle-5.2 b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 new file mode 100644 index 000000000000..09bf2762e667 --- /dev/null +++ b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 @@ -0,0 +1,15 @@ +DEFINED_PHASES=configure install prepare setup +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Maximum likelihood analysis for nucleotide, amino acid, and two-state data +EAPI=4 +HOMEPAGE=http://www.tree-puzzle.de +IUSE=mpi +KEYWORDS=~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-2 +RDEPEND=mpi? ( virtual/mpi ) +RESTRICT=test +SLOT=0 +SRC_URI=http://www.tree-puzzle.de/tree-puzzle-5.2.tar.gz +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_configure:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=9eb444bfbd258f8fbff3201843269bca diff --git a/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r2 b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r2 new file mode 100644 index 000000000000..3b3707a06f46 --- /dev/null +++ b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=x11-libs/wxGTK:2.8[X] +DESCRIPTION=A phylogenetic tree viewer +EAPI=2 +HOMEPAGE=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/wxGTK:2.8[X] +SLOT=0 +SRC_URI=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb wxwidgets 9b34ce3ca77f4e418e8fd9951c4c1cb1 +_md5_=463bdbd7d7491edb402c46e04872d6d4 diff --git a/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 new file mode 100644 index 000000000000..44d5c2dfd195 --- /dev/null +++ b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=prepare +DEPEND=x11-libs/wxGTK:3.0[X] !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A phylogenetic tree viewer +EAPI=5 +HOMEPAGE=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/wxGTK:3.0[X] +SLOT=0 +SRC_URI=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz +_eclass_exported_funcs=src_prepare:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb wxwidgets 9b34ce3ca77f4e418e8fd9951c4c1cb1 +_md5_=94801ab4d28dd1634e87d8bf16363fc6 diff --git a/metadata/md5-cache/sci-biology/trf-4.04 b/metadata/md5-cache/sci-biology/trf-4.04 new file mode 100644 index 000000000000..fc9b22837e44 --- /dev/null +++ b/metadata/md5-cache/sci-biology/trf-4.04 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install unpack +DESCRIPTION=Tandem Repeats Finder +EAPI=4 +HOMEPAGE=http://tandem.bu.edu/trf/trf.html +KEYWORDS=amd64 x86 +LICENSE=trf +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=http://tandem.bu.edu/trf/downloads/trf404.linux +_eclass_exported_funcs=src_unpack:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=406c2b2b8a1c6b562b03f9449a9ff93c diff --git a/metadata/md5-cache/sci-biology/trnascan-se-1.23-r2 b/metadata/md5-cache/sci-biology/trnascan-se-1.23-r2 new file mode 100644 index 000000000000..cbcb85221e29 --- /dev/null +++ b/metadata/md5-cache/sci-biology/trnascan-se-1.23-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare test +DEPEND=dev-lang/perl +DESCRIPTION=tRNA detection in large-scale genome sequences +EAPI=3 +HOMEPAGE=http://lowelab.ucsc.edu/tRNAscan-SE/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=mirror://gentoo/trnascan-se-1.23.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=058be692c482156e6c3af40ff90b77f3 diff --git a/metadata/md5-cache/sci-biology/trnascan-se-1.31 b/metadata/md5-cache/sci-biology/trnascan-se-1.31 new file mode 100644 index 000000000000..c492974d7c89 --- /dev/null +++ b/metadata/md5-cache/sci-biology/trnascan-se-1.31 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare test unpack +DEPEND=dev-lang/perl:=[-build(-)] +DESCRIPTION=tRNA detection in large-scale genome sequences +EAPI=5 +HOMEPAGE=http://lowelab.ucsc.edu/tRNAscan-SE/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> trnascan-se-1.31.tar.gz +_eclass_exported_funcs=src_unpack:unpacker src_prepare:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be 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99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=4ce1a7d2ea0e053f87b43de98d267b9c diff --git a/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 new file mode 100644 index 000000000000..1d8b8acbe391 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install postinst prepare prerm setup +DEPEND=app-arch/unzip !<sci-biology/ucsc-genome-browser-223 mysql? ( virtual/mysql ) server? ( virtual/httpd-cgi ) >=app-admin/webapp-config-1.50.15 +DESCRIPTION=The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath +EAPI=5 +HOMEPAGE=http://genome.ucsc.edu/ +IUSE=+mysql +server static-libs vhosts +KEYWORDS=~amd64 ~x86 +LICENSE=blat +RDEPEND=app-arch/unzip !<sci-biology/ucsc-genome-browser-223 mysql? ( virtual/mysql ) server? ( virtual/httpd-cgi ) >=app-admin/webapp-config-1.50.15 +REQUIRED_USE=server? ( mysql ) +SLOT=0 +SRC_URI=http://hgdownload.cse.ucsc.edu/admin/jksrc.v260.zip +_eclass_exported_funcs=pkg_prerm:webapp pkg_postinst:- pkg_setup:webapp src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb webapp 42c6ef7af496b228f9854b3c81e4b226 +_md5_=291204ab910d7f2b77d52afc8fcb6675 diff --git a/metadata/md5-cache/sci-biology/unafold-3.8 b/metadata/md5-cache/sci-biology/unafold-3.8 new file mode 100644 index 000000000000..62a19cb28510 --- /dev/null +++ b/metadata/md5-cache/sci-biology/unafold-3.8 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Unified Nucleic Acid Folding and hybridization package +EAPI=3 +HOMEPAGE=http://mfold.rna.albany.edu/ +KEYWORDS=~amd64 ~x86 +LICENSE=unafold +SLOT=0 +SRC_URI=http://dinamelt.bioinfo.rpi.edu/download/unafold-3.8.tar.bz2 +_eclass_exported_funcs=src_prepare:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=2d1fd089d7fa16c17dc630855c23d919 diff --git a/metadata/md5-cache/sci-biology/unafold-3.8-r1 b/metadata/md5-cache/sci-biology/unafold-3.8-r1 new file mode 100644 index 000000000000..c5d7b1357d9e --- /dev/null +++ b/metadata/md5-cache/sci-biology/unafold-3.8-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DESCRIPTION=Unified Nucleic Acid Folding and hybridization package +EAPI=5 +HOMEPAGE=http://mfold.rna.albany.edu/ +IUSE=custom-cflags +KEYWORDS=~amd64 ~x86 +LICENSE=unafold +SLOT=0 +SRC_URI=http://dinamelt.bioinfo.rpi.edu/download/unafold-3.8.tar.bz2 +_eclass_exported_funcs=src_prepare:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb 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+_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=0ad9661449bafe761159d8c78957d756 diff --git a/metadata/md5-cache/sci-biology/vaal-46233-r2 b/metadata/md5-cache/sci-biology/vaal-46233-r2 new file mode 100644 index 000000000000..af975862c362 --- /dev/null +++ b/metadata/md5-cache/sci-biology/vaal-46233-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare +DEPEND=!sci-biology/allpaths !sci-biology/allpathslg dev-libs/boost !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Algorithm for detecting SNPs, indels, and other polymorphisms +EAPI=6 +HOMEPAGE=http://www.broadinstitute.org/science/programs/genome-biology/crd/ +IUSE=openmp +KEYWORDS=~amd64 +LICENSE=Whitehead-MIT +RDEPEND=!sci-biology/allpaths !sci-biology/allpathslg +SLOT=0 +SRC_URI=ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/vaal-46233.tar.gz ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc +_eclass_exported_funcs=src_prepare:- src_configure:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=a1c2d330ae12a66a3df20e7f8cd20509 diff --git a/metadata/md5-cache/sci-biology/vcftools-0.1.12b b/metadata/md5-cache/sci-biology/vcftools-0.1.12b new file mode 100644 index 000000000000..018edbc943a4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/vcftools-0.1.12b @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare unpack +DEPEND=lapack? ( virtual/lapack ) virtual/pkgconfig dev-lang/perl:=[-build(-)] +DESCRIPTION=Tools for working with VCF (Variant Call Format) files +EAPI=5 +HOMEPAGE=http://vcftools.sourceforge.net/ +IUSE=lapack +KEYWORDS=~x86 ~amd64 +LICENSE=LGPL-3 +RDEPEND=lapack? ( virtual/lapack ) dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=mirror://sourceforge/vcftools/vcftools_0.1.12b.tar.gz +_eclass_exported_funcs=src_unpack:unpacker src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=7368863377355bc85918b2e59c46abee diff --git a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 new file mode 100644 index 000000000000..27dfd907c217 --- /dev/null +++ b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install postinst prepare +DEPEND=sys-libs/zlib doc? ( virtual/latex-base ) +DESCRIPTION=A sequence assembler for very short reads +EAPI=4 +HOMEPAGE=http://www.ebi.ac.uk/~zerbino/velvet/ +IUSE=-doc +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib +SLOT=0 +SRC_URI=http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.0.18.tgz +_eclass_exported_funcs=pkg_postinst:- src_prepare:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=c6306e29894355e18255d2d534627ead diff --git a/metadata/md5-cache/sci-biology/velvet-1.2.10 b/metadata/md5-cache/sci-biology/velvet-1.2.10 new file mode 100644 index 000000000000..1b8994007bff --- /dev/null +++ b/metadata/md5-cache/sci-biology/velvet-1.2.10 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=doc? ( virtual/latex-base ) +DESCRIPTION=A sequence assembler for very short reads +EAPI=5 +HOMEPAGE=http://www.ebi.ac.uk/~zerbino/velvet/ +IUSE=doc openmp +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e flag-o-matic d270fa247153df66074f795fa42dba3e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=6c8dee8e74b9fb4e57c4bc7e7bc7c782 diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 new file mode 100644 index 000000000000..0ab1b46f5c0a --- /dev/null +++ b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? 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( || ( python_targets_python2_7 ) ) +SLOT=0 +SRC_URI=http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-2.1.1.tar.gz +_eclass_exported_funcs=src_unpack:perl-module src_prepare:- src_configure:- src_compile:- src_test:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb distutils-r1 4e8ac1ba76ddacd8f7c0289aa586a34c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=3bb953b2944fc7a1b3e08ac636074e7f diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.8 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.8 new file mode 100644 index 000000000000..d997d815cb35 --- /dev/null +++ b/metadata/md5-cache/sci-biology/vienna-rna-2.1.8 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-lang/perl media-libs/gd doc? 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( || ( python_targets_python2_7 ) ) +SLOT=0 +SRC_URI=http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz +_eclass_exported_funcs=src_unpack:perl-module src_prepare:- src_configure:- src_compile:- src_test:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c autotools-utils 419811142edf3516b0d0cf1a254d93cb distutils-r1 4e8ac1ba76ddacd8f7c0289aa586a34c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multibuild 742139c87a9fa3766f0c2b155e5522bf multilib 23ae8c186171e6476af098d2a50d0ee0 multiprocessing e32940a7b2a9992ad217eccddb84d548 perl-functions aac50de73be0a80ebe780e0b20850130 perl-module 461f1d9eb930e8d1b178a39e83635fd0 python-r1 0f6937650a475d673baa5d0c8c0b37b3 python-utils-r1 2e6826f6a93ad2acf904eecf5b5fb6d2 toolchain-funcs d513d423d449877e49d99af3f7af7acb unpacker 45d07319df5f40ee6af58418b0f930be +_md5_=46d668ebb720105ba3b35746683b2969 diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-5.4 b/metadata/md5-cache/sci-biology/wgs-assembler-5.4 new file mode 100644 index 000000000000..869c727f14e3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/wgs-assembler-5.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install +DEPEND=x11-libs/libXt !x11-terms/terminator +DESCRIPTION=A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG +EAPI=2 +HOMEPAGE=http://sourceforge.net/projects/wgs-assembler/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl +SLOT=0 +SRC_URI=mirror://sourceforge/wgs-assembler/wgs-5.4.tar.bz2 +_eclass_exported_funcs=src_configure:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=5c4f55f3feb698755af3af2b54cabd70 diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-6.1 b/metadata/md5-cache/sci-biology/wgs-assembler-6.1 new file mode 100644 index 000000000000..fd6578b0101d --- /dev/null +++ b/metadata/md5-cache/sci-biology/wgs-assembler-6.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install +DEPEND=x11-libs/libXt !x11-terms/terminator +DESCRIPTION=A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG +EAPI=2 +HOMEPAGE=http://sourceforge.net/projects/wgs-assembler/ +KEYWORDS=~amd64 x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl +SLOT=0 +SRC_URI=mirror://sourceforge/wgs-assembler/wgs-6.1.tar.bz2 +_eclass_exported_funcs=src_configure:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=f316356c9f780f64d9a495cb671c1b33 diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-7.0 b/metadata/md5-cache/sci-biology/wgs-assembler-7.0 new file mode 100644 index 000000000000..e9ba920ee667 --- /dev/null +++ b/metadata/md5-cache/sci-biology/wgs-assembler-7.0 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install +DEPEND=x11-libs/libXt !x11-terms/terminator +DESCRIPTION=A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG +EAPI=2 +HOMEPAGE=http://sourceforge.net/projects/wgs-assembler/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl +SLOT=0 +SRC_URI=mirror://sourceforge/wgs-assembler/wgs-7.0.tar.bz2 +_eclass_exported_funcs=src_configure:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=abcdb729169ae5b79e27d5137ad6169a diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1 b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1 new file mode 100644 index 000000000000..cd4cd0828d15 --- /dev/null +++ b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare setup +DEPEND=x11-libs/libXt !x11-terms/terminator =dev-lang/python-2* +DESCRIPTION=A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG +EAPI=4 +HOMEPAGE=http://sourceforge.net/projects/wgs-assembler/ +IUSE=static-libs +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl =dev-lang/python-2* +SLOT=0 +SRC_URI=mirror://sourceforge/wgs-assembler/wgs-7.0.tar.bz2 +_eclass_exported_funcs=pkg_setup:- src_prepare:- src_configure:- src_compile:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 python efc1c55fc44c5b7272fc2ffba73c3e6f toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=66b0a3d64fe0cb82bc56cd4d19962722 diff --git a/metadata/md5-cache/sci-biology/wise-2.4.0_alpha b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha new file mode 100644 index 000000000000..b46d0025e65f --- /dev/null +++ b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=~sci-biology/hmmer-2.3.2 app-shells/tcsh dev-lang/perl virtual/latex-base +DESCRIPTION=Intelligent algorithms for DNA searches +EAPI=5 +HOMEPAGE=http://www.ebi.ac.uk/Wise2/ +IUSE=doc static-libs +KEYWORDS=~alpha amd64 ia64 ~sparc x86 +LICENSE=BSD +RDEPEND=~sci-biology/hmmer-2.3.2 +SLOT=0 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/wise2/wise2.4.0alpha.tar.gz +_eclass_exported_funcs=src_prepare:- src_compile:- src_test:- src_install:- +_eclasses_=eutils 9d81603248f2ba3ec59124320d123e5e multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb versionator 99ae9d758cbe7cfed19170e7d48f5a9c +_md5_=8eee710efb6992b2ba447f3f5b941f08 diff --git a/metadata/md5-cache/sci-biology/yass-1.14 b/metadata/md5-cache/sci-biology/yass-1.14 new file mode 100644 index 000000000000..671eab611d81 --- /dev/null +++ b/metadata/md5-cache/sci-biology/yass-1.14 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=Genomic similarity search with multiple transition constrained spaced seeds +EAPI=2 +HOMEPAGE=http://bioinfo.lifl.fr/yass/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://bioinfo.lifl.fr/yass/files/yass-1.14.tar.gz +_eclass_exported_funcs=src_install:- +_md5_=29504b025b5aa446aba4231cc72d631c diff --git a/metadata/md5-cache/sci-biology/yass-1.14-r1 b/metadata/md5-cache/sci-biology/yass-1.14-r1 new file mode 100644 index 000000000000..24c8883d2a24 --- /dev/null +++ b/metadata/md5-cache/sci-biology/yass-1.14-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dmalloc? ( dev-libs/dmalloc ) !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Genomic similarity search with multiple transition constrained spaced seeds +EAPI=2 +HOMEPAGE=http://bioinfo.lifl.fr/yass/ +IUSE=dmalloc lowmem threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dmalloc? ( dev-libs/dmalloc ) +SLOT=0 +SRC_URI=http://bioinfo.lifl.fr/yass/files/yass-1.14.tar.gz +_eclass_exported_funcs=src_prepare:- src_configure:- src_install:- +_eclasses_=autotools 07e71b3b5690738ef7e8bc097077e00c eutils 9d81603248f2ba3ec59124320d123e5e libtool 4890219c51da247200223277f993e054 multilib 23ae8c186171e6476af098d2a50d0ee0 toolchain-funcs d513d423d449877e49d99af3f7af7acb +_md5_=3d35f51c9a16817738548340df88ad12 |