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* sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2David Seifert2016-10-093-0/+205
| | | | | | | | | Gentoo-bug: 328911, 586960 * EAPI=6 * Introduce SLOT=2 and rename binaries and static libraries Package-Manager: portage-2.3.1
* sci-biology/hmmer: Version bump to 3.1_beta2David Seifert2016-10-094-0/+470
| | | | | | | | * EAPI=6 * Make perl shebangs portable * Install headers into 'hmmer3' subdir Package-Manager: portage-2.3.1
* sci-biology/tophat: Do not wrap scriptsDavid Seifert2016-10-031-2/+2
| | | | Package-Manager: portage-2.3.1
* sci-biology/samtools: Use 'python-single-r1' instead of 'python-r1'David Seifert2016-10-031-17/+21
| | | | Package-Manager: portage-2.3.1
* sci-biology/consed: Remove old ebuildsDavid Seifert2016-10-033-165/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/consed: Version bump to 29David Seifert2016-10-036-0/+1662
| | | | | | | | | | * EAPI=6 * Allow for compiling with GCC 6 * [QA] Respect all user variables (CC, CXX, ...) * [QA] Fix various C and C++ related warnings * Fix perl shebangs to be portable Package-Manager: portage-2.3.1
* sci-biology/phrap: Revbump to EAPI=6David Seifert2016-10-033-6/+112
| | | | Package-Manager: portage-2.3.1
* sci-biology/phred: Revbump to EAPI=6David Seifert2016-10-035-41/+170
| | | | Package-Manager: portage-2.3.1
* sci-biology/tophat: Remove old and ancient 1.0 ebuildsDavid Seifert2016-09-272-39/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/rebase: amd64 stable wrt bug #590146Agostino Sarubbo2016-09-261-1/+1
| | | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/biopython: amd64 stable wrt bug #584210Agostino Sarubbo2016-09-261-1/+1
| | | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/treeviewx: amd64 stable wrt bug #584034Agostino Sarubbo2016-09-261-1/+1
| | | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/tophat: USE="threads" dep on dev-libs/boostDavid Seifert2016-09-252-8/+61
| | | | | | | | Gentoo-bug: 594810 * Remove autoconf macros from archive, depend on sys-devel/autoconf instead for the latest versions. Package-Manager: portage-2.3.1
* sci-biology/vcftools: Add missing RDEPEND on sys-libs/zlibDavid Seifert2016-09-251-1/+2
| | | | Package-Manager: portage-2.3.1
* sci-biology/vcftools: Remove old ebuildDavid Seifert2016-09-253-99/+0
| | | | | | | Package-Manager: portage-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/2407 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/vcftools: Version bump to 0.1.14David Seifert2016-09-253-0/+90
| | | | | | | | | | | Gentoo-bug: 594924 * EAPI=6 * Properly RDEPEND on dev-lang/perl Package-Manager: portage-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/2407 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Add missing RDEPEND on sys-libs/zlibDavid Seifert2016-09-251-0/+1
| | | | Package-Manager: portage-2.3.1
* sci-biology/bedtools: Remove old ebuildsDavid Seifert2016-09-253-68/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/bedtools: Version bump to 2.26.0David Seifert2016-09-253-0/+912
| | | | | | | | | | | Gentoo-bug: 594994 * EAPI=6 * Make buildsystem output verbose * Inherit 'python-any-r1', due to python script * Add dependencies for test suite * Properly set CXX and CXXFLAGS Package-Manager: portage-2.3.1
* sci-biology/amos: Allow for compiling with GCC 6David Seifert2016-09-244-37/+185
| | | | | | | | Gentoo-bug: 594928 * EAPI=6 * [QA] fix implicit declarations Package-Manager: portage-2.3.1
* sci-biology/eugene: Bump to 4.1d from science-overlayDavid Seifert2016-09-244-0/+144
| | | | | | | | Gentoo-bug: 594700 * EAPI=6 * Fix -Wformat warnings Package-Manager: portage-2.3.1
* sci-biology/iqpnni: Remove old ebuildsDavid Seifert2016-09-243-61/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/iqpnni: Port to EAPI=6David Seifert2016-09-241-0/+31
| | | | Package-Manager: portage-2.3.1
* sci-biology/iqpnni: Fix CRLF line endings in patchDavid Seifert2016-09-241-24/+24
| | | | | | Gentoo-bug: 594654 Package-Manager: portage-2.3.1
* sci-biology/clustal-omega: Version bump, allow for compiling with GCC 6David Seifert2016-09-223-3/+36
| | | | | | Gentoo-bug: 594692 Package-Manager: portage-2.3.1
* sci-biology/tophat: Allow for compiling with GCC 6David Seifert2016-09-222-0/+15
| | | | | | Gentoo-bug: 594544 Package-Manager: portage-2.3.1
* sci-biology/iqpnni: fix cpp14 compilation; bug #594332Kacper Kołodziej2016-09-202-0/+54
| | | | | | Closes: https://github.com/gentoo/gentoo/pull/2365 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/prank: Remove old ebuildsDavid Seifert2016-09-204-89/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/prank: Allow for compiling with GCC 6David Seifert2016-09-202-3/+19
| | | | | | | Gentoo-bug: 594060 * EAPI=6 Package-Manager: portage-2.3.1
* sci-biology/abyss: pin boost subslot, noticed by SoapSergei Trofimovich2016-09-181-1/+1
| | | | Package-Manager: portage-2.3.0
* sci-biology/bowtie: Allow for compiling with GCC 6David Seifert2016-09-192-1/+31
| | | | | | Gentoo-bug: 593966 Package-Manager: portage-2.3.0
* sci-biology/abyss: bump up to 1.9.0, tweak for gcc-6, bug #594254Sergei Trofimovich2016-09-184-0/+106
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | On gcc-6 build failed as: ``` In file included from AssemblyAlgorithms.cpp:4:0: ../DataLayer/FastaReader.h: In member function ‘FastaReader::operator void*() const’: ../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ ... operator void*() const { return m_in; } ^~~~ ``` In the following source: ```c++ static bool existFile(const char* f) { ifstream file(f); return file; } ``` c++98 provides file->operator void*() c++11 provides file->explicit operator bool() Hence the failure on c++11. The change adds explicit casts around ifstream. Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/594254 Package-Manager: portage-2.3.0
* sci-biology/lagan: Remove old ebuildsDavid Seifert2016-09-182-105/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/lagan: Allow for compiling with GCC 6David Seifert2016-09-183-0/+641
| | | | | | | | | Gentoo-bug: 594148 * EAPI=6 * Also fix QA violations due to implicit declarations and incorrectly formatted fprintf calls. Package-Manager: portage-2.3.0
* sci-biology/rebase: Version BumpJustin Lecher2016-09-102-0/+47
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/mosaik: Version bump to 2.2.30David Seifert2016-09-045-0/+374
| | | | | | | | | | * EAPI=6 * Make build system verbose * Honour CPPFLAGS and LDFLAGS * Handle LFS properly * Fix -Werror=format-security errors Package-Manager: portage-2.3.0
* sci-biology/mafft: Version bump to 7.305David Seifert2016-09-042-0/+70
| | | | | | * EAPI=6 Package-Manager: portage-2.3.0
* sci-biology/yass: remove deprecated EAPI ebuildsDavid Seifert2016-09-042-58/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/yass: Port to EAPI=6David Seifert2016-09-041-0/+33
| | | | Package-Manager: portage-2.3.0
* sci-biology/biopython: Version bumpDavid Seifert2016-09-032-0/+57
| | | | Package-Manager: portage-2.3.0
* sci-biology/bwa: Version bump to 0.7.15David Seifert2016-09-033-7/+6
| | | | Package-Manager: portage-2.3.0
* sci-biology/tophat: Various QA fixes, handle python properlyDavid Seifert2016-09-031-4/+14
| | | | | | | | | | * Add subslot operator := for dev-libs/boost * DEPEND on virtual/pkgconfig * Add missing ${PYTHON_REQUIRED_USE} and ${PYTHON_DEPS} * Install python scripts and modules properly using 'python_doscript' and 'python_domodule' Package-Manager: portage-2.3.0
* sci-biology/allpathslg: Unconditionally require OpenMP supportDavid Seifert2016-08-131-10/+17
| | | | | | | | | Gentoo-bug: 591166 * The configure script of sci-biology/allpathslg allows for specifying --enable/--disable-openmp, without it actually being optional. Package-Manager: portage-2.3.0
* sci-biology/finchtv: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/fasta: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/exonerate: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/ApE: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/rebase: Version BumpJustin Lecher2016-07-312-0/+47
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/seaview: version bumpDavid Seifert2016-07-312-0/+79
| | | | | | * EAPI=6 Package-Manager: portage-2.3.0
* sci-biology/seqan: version bumpDavid Seifert2016-07-302-2/+4
| | | | Package-Manager: portage-2.3.0