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* sci-biology/lagan: Allow for compiling with GCC 6David Seifert2016-09-18
| | | | | | | | | 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 Lecher2016-09-10
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/mosaik: Version bump to 2.2.30David Seifert2016-09-04
| | | | | | | | | | * 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 Seifert2016-09-04
| | | | | | * EAPI=6 Package-Manager: portage-2.3.0
* sci-biology/yass: remove deprecated EAPI ebuildsDavid Seifert2016-09-04
| | | | Package-Manager: portage-2.3.0
* sci-biology/yass: Port to EAPI=6David Seifert2016-09-04
| | | | Package-Manager: portage-2.3.0
* sci-biology/biopython: Version bumpDavid Seifert2016-09-03
| | | | Package-Manager: portage-2.3.0
* sci-biology/bwa: Version bump to 0.7.15David Seifert2016-09-03
| | | | Package-Manager: portage-2.3.0
* sci-biology/tophat: Various QA fixes, handle python properlyDavid Seifert2016-09-03
| | | | | | | | | | * 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 Seifert2016-08-13
| | | | | | | | | 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 Ramos2016-08-06
| | | | Package-Manager: portage-2.3.0
* sci-biology/fasta: Cleanup per bug #146900Pacho Ramos2016-08-06
| | | | Package-Manager: portage-2.3.0
* sci-biology/exonerate: Cleanup per bug #146900Pacho Ramos2016-08-06
| | | | Package-Manager: portage-2.3.0
* sci-biology/ApE: Cleanup per bug #146900Pacho Ramos2016-08-06
| | | | Package-Manager: portage-2.3.0
* sci-biology/rebase: Version BumpJustin Lecher2016-07-31
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/seaview: version bumpDavid Seifert2016-07-31
| | | | | | * EAPI=6 Package-Manager: portage-2.3.0
* sci-biology/seqan: version bumpDavid Seifert2016-07-30
| | | | Package-Manager: portage-2.3.0
* sci-biology/emboss: add a blocker for games-action/xbomber #589918Austin English2016-07-28
| | | | | | Gentoo-Bug: https://bugs.gentoo.org/589918 Package-Manager: portage-2.3.0
* sourceforge: switch to https:// URIsMike Frysinger2016-07-27
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* sci-biology/bioruby: add ruby21Hans de Graaff2016-07-22
| | | | Package-Manager: portage-2.2.28
* sci-biology/clustal-omega: Unconditionally prune .la filesDavid Seifert2016-07-02
| | | | Package-Manager: portage-2.3.0
* sci-biology/clustal-omega: Version BumpJustin Lecher2016-07-02
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Bump to latest versionJustin Lecher2016-07-02
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bowtie: version bumpDavid Seifert2016-06-04
| | | | Package-Manager: portage-2.3.0_rc1
* sci-biology/foldingathome: use #!/sbin/openrc-run instead of #!/sbin/runscriptAustin English2016-05-18
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* sci-biology/abyss: add missing dev-libs/boost dependencySergei Trofimovich2016-05-15
| | | | Package-Manager: portage-2.2.28
* sci-biology/vienna-rna: Fix QA MissingSlotDepDavid Seifert2016-05-15
| | | | Package-Manager: portage-2.2.28
* sci-biology/vienna-rna: Fix QA MissingSlotDepDavid Seifert2016-05-15
| | | | Package-Manager: portage-2.2.28
* sci-biology/mrbayes: Fix QA MissingSlotDepDavid Seifert2016-05-15
| | | | Package-Manager: portage-2.2.28
* sci-biology/bwa: Version bumpDavid Seifert2016-05-08
| | | | Package-Manager: portage-2.2.28
* sci-biology/allpathslg: replace isnan macro with proper std::isnan functionDavid Seifert2016-05-05
| | | | | | Gentoo-Bug: 580086 Package-Manager: portage-2.2.28
* sci-biology/bioperl: Fix dependency on dev-perl/YAMLKent Fredric2016-04-29
| | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="alpha amd64 amd64-fbsd arm arm64 hppa ia64 m68k mips nios2 ppc ppc64 riscv s390 sh sparc sparc-fbsd x86 x86-fbsd"
* sci-biology/emboss: Clean up of files dirJustin Lecher2016-04-26
| | | | | | | | | Move to readme.gentoo-r1.eclass Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=579728 Package-Manager: portage-2.2.28 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/hmmer: cheamup of 2.3.2 versionIan Stakenvicius2016-04-19
| | | | | | | | | * Bumped EAPI * Merged KEYWORDS between 2.3.2-r1 and 2.3.2-r2 * dropped IUSE="pvm" as package was dropped 5 years ago * fixed metadata.xml to match Package-Manager: portage-2.2.26
* sci-biology/bioperl: Fix dependency on dev-perl/Set-ScalarKent Fredric2016-04-15
| | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64 amd64-fbsd arm arm64 mips nios2 ppc ppc64 riscv s390 sh sparc-fbsd"
* sci-biology/goby: Clean up old.Patrice Clement2016-04-15
| | | | Package-Manager: portage-2.2.26
* sci-biology/goby: Bump fastutil dependency SLOT to 0.Patrice Clement2016-04-15
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* sci-biology/bowtie: Version bump to 2.2.8David Seifert2016-04-10
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/samtools: Remove lua dep, fix perl shebangsDavid Seifert2016-04-10
| | | | Package-Manager: portage-2.2.28
* sci-biology/pysam: Remove oldDavid Seifert2016-04-10
| | | | Package-Manager: portage-2.2.28
* sci-biology/pysam: Version bump, add py3 supportDavid Seifert2016-04-10
| | | | Package-Manager: portage-2.2.28
* sci-biology/samtools: Remove lua dep, fix perl shebangsDavid Seifert2016-04-09
| | | | Package-Manager: portage-2.2.28
* sci-biology/seqan: Remove old and broken ebuildsDavid Seifert2016-04-09
| | | | Package-Manager: portage-2.2.28
* sci-biology/tophat: Remove old and brokenDavid Seifert2016-04-09
| | | | Package-Manager: portage-2.2.28
* sci-biology/tophat: Version bump, use samtools:0.1-legacyDavid Seifert2016-04-09
| | | | | | | | | Gentoo-Bug: 545154, 546816, 566494, 572054 * EAPI=6 * Unbundle samtools and SeqAn * Fix broken shebangs in python scripts Package-Manager: portage-2.2.28
* sci-biology/bowtie: unbundle SeqAn, import Debian patchesDavid Seifert2016-04-09
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/seqan: SLOT 1.4 and 2.1, allow for parallel installationDavid Seifert2016-04-09
| | | | | | | Gentoo-Bug: 566502 * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/readseq: Remove dead package, see bug #550148James Le Cuirot2016-04-03
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* sci-biology/abyss: Remove oldDavid Seifert2016-04-03
| | | | Package-Manager: portage-2.2.28
* sci-biology/abyss: Latest ebuild from science-overlayDavid Seifert2016-04-03
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
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