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-rw-r--r--sci-biology/mummer/Manifest4
-rw-r--r--sci-biology/mummer/files/3.22-ldflags.patch16
-rw-r--r--sci-biology/mummer/files/3.22-prll.patch56
-rw-r--r--sci-biology/mummer/files/mummer-3.20-gcc43.patch12
-rw-r--r--sci-biology/mummer/mummer-3.20.ebuild57
-rw-r--r--sci-biology/mummer/mummer-3.21.ebuild52
-rw-r--r--sci-biology/mummer/mummer-3.22-r1.ebuild63
-rw-r--r--sci-biology/mummer/mummer-3.9.4_alpha.ebuild82
8 files changed, 0 insertions, 342 deletions
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
index e752ce6907b5..53c34cf4516c 100644
--- a/sci-biology/mummer/Manifest
+++ b/sci-biology/mummer/Manifest
@@ -1,5 +1 @@
-DIST MUMmer3.20.tar.gz 3155446 SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260 SHA512 7c80bb605d57739809eb1b1cf8a579d72048e510362237d9ba64e21be18cc663769cda5dabc287832e59fb62804df34bc8336c2b42474466e7ee1e126848aecd WHIRLPOOL a08af35aee960bcd6274d3a00b1c1819d23367c81a72fd41c652c3579253b0aeeb5ef66f6dcfed60b4987c3a40830d04cd81745dce8a274cc3de0663dd54ae6f
-DIST MUMmer3.21.tar.gz 3155965 SHA256 7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8 SHA512 61d49e5451e1697003f7acaac690f2ede7ab71766208d3218954527c48be76ddb78d60ff40ae1bdcd4b93d3efaf21b5bd027da3722eab1ae3fa399ee726bc96e WHIRLPOOL 50c7b0d7c00bf85aa8e0f8b80bf55186f8c0a53d26c3e50d2149120bc46f3632de4cb861a4d4265c1e3be731dffb71940344b238fd3e977412134b0e401cb95e
-DIST MUMmer3.22.tar.gz 3156338 SHA256 429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da SHA512 37bbb368c679d2e98fa9b9ef10c18008c173c25ee79183eb30e34125b1dc9cd10f005b7bd7c648335a8025509d8e3456fcc7ce497c95fa71c3c5d3ed3685665f WHIRLPOOL 487333ca38a9c59984ed059e8dd620ad3c0a5ae1a537e500c7b8b2d58213ac88960a13c0f25e6e0490d1209c9e73cfe8df0f8a43dbae9fd6a3e9fe3ce42da453
DIST MUMmer3.23.tar.gz 3160143 SHA256 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3 WHIRLPOOL 7471d20a88f5ddf510d1e4826480706a683f005f3bab21ebb19b1fcba2c8f431435cce27a1cdf98ece8d4bb4dafcc349362037f6d526db3f564b7c013c67e882
-DIST mummer-3.9.4_alpha.tar.gz 956517 SHA256 fb2f03c729cd078d526d6318f91061f8832c2e8bd0d519ddf3c0b6e656029cfa SHA512 f0b962a69df6918afc7d163b30bcf5bd9eb2be663c8ac685b5e06317953cf12b9d240df8a5bfe8a9410b65cf88176cc7a71eecfc460e51df7ad1b27dc3a10fc2 WHIRLPOOL 8443cde87f868136eaa005db2b5b461a822097778d4c36448602a5cda058dc1dfa10daa08883248ffaba79a1d33240170b94b96548ebb56a01eaa27838d4afd6
diff --git a/sci-biology/mummer/files/3.22-ldflags.patch b/sci-biology/mummer/files/3.22-ldflags.patch
deleted file mode 100644
index d3c4a60a1adb..000000000000
--- a/sci-biology/mummer/files/3.22-ldflags.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/src/tigr/Makefile b/src/tigr/Makefile
-index cf6b9ca..5b28d1e 100644
---- a/src/tigr/Makefile
-+++ b/src/tigr/Makefile
-@@ -9,9 +9,9 @@ AUX_BIN_DIR := $(CURDIR)
- endif
-
- OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
--BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
-+BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
- chmod 755 $(BIN_DIR)/$@
--AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
-+AUX_BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
- chmod 755 $(AUX_BIN_DIR)/$@
- VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
-
diff --git a/sci-biology/mummer/files/3.22-prll.patch b/sci-biology/mummer/files/3.22-prll.patch
deleted file mode 100644
index 3b24ee40214a..000000000000
--- a/sci-biology/mummer/files/3.22-prll.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 4db4977..bbd00ed 100644
---- a/Makefile
-+++ b/Makefile
-@@ -114,15 +114,15 @@ install: all
-
-
- kurtz:
-- cd $(KURTZ_SRC_DIR); $(MAKE) mummer
-+ $(MAKE) -C $(KURTZ_SRC_DIR) mummer
-
-
- scripts:
-- cd $(SCRIPT_DIR); $(MAKE) all
-+ $(MAKE) -C $(SCRIPT_DIR) all
-
-
- tigr:
-- cd $(TIGR_SRC_DIR); $(MAKE) all
-+ $(MAKE) -C $(TIGR_SRC_DIR) all
-
-
- uninstall: clean
-diff --git a/src/kurtz/Makefile b/src/kurtz/Makefile
-index 85dfc16..5bff793 100644
---- a/src/kurtz/Makefile
-+++ b/src/kurtz/Makefile
-@@ -1,7 +1,7 @@
- all:
-- cd libbasedir; $(MAKE) all
-- cd streesrc; $(MAKE) all
-- cd mm3src; $(MAKE) all
-+ $(MAKE) -C libbasedir all
-+ $(MAKE) -C streesrc all
-+ $(MAKE) -C mm3src all
-
- clean:
- rm -f *~
-@@ -10,11 +10,11 @@ clean:
- cd mm3src; $(MAKE) clean
-
- mummer:
-- cd libbasedir; $(MAKE) libbase.a
-- cd streesrc; $(MAKE) libstree.a
-- cd mm3src; $(MAKE) mummer
-+ $(MAKE) -C libbasedir libbase.a
-+ $(MAKE) -C streesrc libstree.a
-+ $(MAKE) -C mm3src mummer
-
- splintall:
-- cd libbasedir; ${MAKE} splintall
-- cd streesrc; ${MAKE} splintall
-- cd mm3src; ${MAKE} splintall
-+ $(MAKE) -C libbasedir splintall
-+ $(MAKE) -C streesrc splintall
-+ $(MAKE) -C mm3src splintall
diff --git a/sci-biology/mummer/files/mummer-3.20-gcc43.patch b/sci-biology/mummer/files/mummer-3.20-gcc43.patch
deleted file mode 100644
index 4d3edb41e46a..000000000000
--- a/sci-biology/mummer/files/mummer-3.20-gcc43.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/tigr/show-diff.cc.orig 2008-06-16 17:55:34.000000000 +0000
-+++ src/tigr/show-diff.cc 2008-06-16 17:56:25.000000000 +0000
-@@ -14,6 +14,8 @@
- #include <cstdlib>
- #include <cassert>
- #include <climits>
-+#include <algorithm>
-+
- using namespace std;
-
-
-
diff --git a/sci-biology/mummer/mummer-3.20.ebuild b/sci-biology/mummer/mummer-3.20.ebuild
deleted file mode 100644
index 737e6d6aa644..000000000000
--- a/sci-biology/mummer/mummer-3.20.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit eutils
-
-MY_P="MUMmer${PV}"
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh"
-
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
- epatch "${FILESDIR}"/${P}-gcc43.patch
- # Warning: package uses CPPFLAGS on c in addition to cpp, despite the name
- sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
- -e 's/LDFLAGS =$//' "${S}/Makefile"
-}
-
-src_compile() {
- emake || die "emake failed"
-
- sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
- -e 's|\(set bindir = \).*|\1/usr/bin|' \
- -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
- -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
- scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths"
- sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
-}
-
-src_install() {
- dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
- exact-tandems promer repeat-match show-aligns gaps mummer \
- show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* || die
- newbin annotate mummer-annotate || die
-
- insinto /usr/share/${PN}/scripts
- doins scripts/{*.awk,*.csh,*.pl}
- insinto /usr/share/${PN}/lib
- doins scripts/Foundation.pm || die
-
- dodoc ACKNOWLEDGEMENTS ChangeLog README
- insinto /usr/share/doc/${PF}
- use doc && doins -r docs
-}
diff --git a/sci-biology/mummer/mummer-3.21.ebuild b/sci-biology/mummer/mummer-3.21.ebuild
deleted file mode 100644
index e9faee09eead..000000000000
--- a/sci-biology/mummer/mummer-3.21.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit eutils
-
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh"
-
-S="${WORKDIR}/MUMmer${PV}"
-
-src_unpack() {
- unpack ${A}
- # Warning: package uses CPPFLAGS on c as well as cpp, despite the name
- sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
- -e 's/LDFLAGS =$//' "${S}/Makefile" || die
-}
-
-src_compile() {
- emake || die
-
- sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
- -e 's|\(set bindir = \).*|\1/usr/bin|' \
- -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
- -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
- scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
- mv annotate mummer-annotate || die
- sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
-}
-
-src_install() {
- dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die
-
- insinto /usr/share/${PN}/scripts
- doins scripts/{*.awk,*.csh,*.pl} || die
- insinto /usr/share/${PN}/lib
- doins scripts/Foundation.pm || die
-
- dodoc ACKNOWLEDGEMENTS ChangeLog README
- insinto /usr/share/doc/${PF}
- use doc && doins -r docs
-}
diff --git a/sci-biology/mummer/mummer-3.22-r1.ebuild b/sci-biology/mummer/mummer-3.22-r1.ebuild
deleted file mode 100644
index f9caede7641a..000000000000
--- a/sci-biology/mummer/mummer-3.22-r1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="3"
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh"
-
-S="${WORKDIR}/MUMmer${PV}"
-
-src_prepare() {
- use amd64 && append-flags -DSIXTYFOURBITS
-
- epatch \
- "${FILESDIR}"/${PV}-prll.patch \
- "${FILESDIR}"/${PV}-ldflags.patch
-
- sed \
- -e '/^CFLAGS/d' \
- -e '/^CXXFLAGS/d' \
- -e '/^LDFLAGS/d' \
- -i Makefile || die
-}
-
-src_compile() {
- emake || die
-
- sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
- -e 's|\(set bindir = \).*|\1/usr/bin|' \
- -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
- -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
- scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
- mv annotate mummer-annotate || die
- sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
-}
-
-src_install() {
- dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die
-
- insinto /usr/share/${PN}/scripts
- doins scripts/{*.awk,*.csh,*.pl} || die
- insinto /usr/share/${PN}/lib
- doins scripts/Foundation.pm || die
-
- dodoc ACKNOWLEDGEMENTS ChangeLog README || die
- insinto /usr/share/doc/${PF}
- if use doc; then
- doins -r docs || die
- fi
-}
diff --git a/sci-biology/mummer/mummer-3.9.4_alpha.ebuild b/sci-biology/mummer/mummer-3.9.4_alpha.ebuild
deleted file mode 100644
index 2865c3d9b2e9..000000000000
--- a/sci-biology/mummer/mummer-3.9.4_alpha.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit perl-functions python-r1 toolchain-funcs
-
-MY_PV=${PV//_/}
-
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="https://github.com/gmarcais/${PN}/releases/download/v${MY_PV}/${PN}-${MY_PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="openmp perl python"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- python? (
- ${PYTHON_DEPS}
- dev-lang/swig:0
- )"
-RDEPEND="
- app-shells/tcsh
- dev-lang/perl:=
- python? ( ${PYTHON_DEPS} )"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S=${WORKDIR}/${PN}-${MY_PV}
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
- use python && preamble="python_foreach_impl run_in_build_dir"
-}
-
-src_configure() {
- perl_set_version
- configure() {
- local pythonconf
- if use python; then
- pythonconf="--enable-python-binding=$(python_get_sitedir)"
- else
- pythonconf="--disable-python-binding"
- fi
-
- ECONF_SOURCE="${S}" econf \
- --disable-static \
- --disable-ruby-binding \
- $(use_enable perl perl-binding "${VENDOR_LIB}") \
- $(use_enable openmp) \
- $(use_enable python swig) \
- "${pythonconf}"
- }
- ${preamble} configure
-}
-
-src_compile() {
- ${preamble} default
-}
-
-src_install() {
- ${preamble} default
- einstalldocs
-
- # avoid file collision
- mv "${ED%/}"/usr/bin/{,mummer-}annotate || die
-
- # move perl module into right place
- mkdir -p "${D%/}${VENDOR_LIB}" || die
- mv "${ED%/}"/usr/$(get_libdir)/mummer/Foundation.pm "${D%/}${VENDOR_LIB}" || die
-
- # no static libs, can purge .la files
- find "${D}" -name '*.la' -delete || die
-}