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* sci-biology/bioperl: Fix dependency on dev-perl/YAMLKent Fredric2016-04-291-1/+1
| | | | | 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 Lecher2016-04-268-838/+7
| | | | | | | | | 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 Stakenvicius2016-04-193-68/+15
| | | | | | | | | * 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 Fredric2016-04-152-4/+4
| | | | | 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 Clement2016-04-152-114/+0
| | | | Package-Manager: portage-2.2.26
* sci-biology/goby: Bump fastutil dependency SLOT to 0.Patrice Clement2016-04-152-0/+114
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* sci-biology/bowtie: Version bump to 2.2.8David Seifert2016-04-102-0/+62
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/samtools: Remove lua dep, fix perl shebangsDavid Seifert2016-04-101-3/+14
| | | | Package-Manager: portage-2.2.28
* sci-biology/pysam: Remove oldDavid Seifert2016-04-102-26/+0
| | | | Package-Manager: portage-2.2.28
* sci-biology/pysam: Version bump, add py3 supportDavid Seifert2016-04-103-0/+87
| | | | Package-Manager: portage-2.2.28
* sci-biology/samtools: Remove lua dep, fix perl shebangsDavid Seifert2016-04-091-1/+11
| | | | Package-Manager: portage-2.2.28
* sci-biology/seqan: Remove old and broken ebuildsDavid Seifert2016-04-095-178/+0
| | | | Package-Manager: portage-2.2.28
* sci-biology/tophat: Remove old and brokenDavid Seifert2016-04-0910-526/+0
| | | | Package-Manager: portage-2.2.28
* sci-biology/tophat: Version bump, use samtools:0.1-legacyDavid Seifert2016-04-093-0/+184
| | | | | | | | | 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 Seifert2016-04-098-0/+700
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/seqan: SLOT 1.4 and 2.1, allow for parallel installationDavid Seifert2016-04-095-0/+186
| | | | | | | Gentoo-Bug: 566502 * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/readseq: Remove dead package, see bug #550148James Le Cuirot2016-04-035-108/+0
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* sci-biology/abyss: Remove oldDavid Seifert2016-04-034-120/+0
| | | | Package-Manager: portage-2.2.28
* sci-biology/abyss: Latest ebuild from science-overlayDavid Seifert2016-04-032-0/+94
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/cufflinks: Remove oldDavid Seifert2016-04-038-1527/+0
| | | | Package-Manager: portage-2.2.28
* sci-biology/cufflinks: Depend only on sci-biology/samtools:0.1-legacyDavid Seifert2016-04-032-0/+83
| | | | | | | | | | Gentoo-Bug: 535716 * EAPI=6 * Updated boost in tree has fixed serialization for boost::shared_ptr * Build system is now orthogonal to sci-biology/samtools:0 and does not block updating to latest samtools Package-Manager: portage-2.2.28
* sci-biology/rebase: amd64/ppc/x86 stable, (ALLARCHES policy) wrt bug #578804Agostino Sarubbo2016-04-021-1/+1
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2016-04-022-0/+47
| | | | | Package-Manager: portage-2.2.27 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/samtools: version bump to 1.3, to match htslibDavid Seifert2016-03-284-0/+998
| | | | | | | | * EAPI=6 * Added modern AX_WITH_CURSES that works with pkg-config * Fixed incorrect symlinks for libbam.so Package-Manager: portage-2.2.28
* sci-biology/samtools: Move to SLOT="0.1-legacy" for future legacy versionsDavid Seifert2016-03-282-11/+11
| | | | Package-Manager: portage-2.2.28
* sci-biology/samtools: Add elog message discouraging direct useDavid Seifert2016-03-281-0/+6
| | | | Package-Manager: portage-2.2.28
* sci-biology/samtools: Version bump to 0.1.20David Seifert2016-03-283-0/+271
| | | | | | | | | * EAPI=6 * samtools will be slotted with SLOT="legacy", in order to be able to install applications that rely on the old monolithic library. Package-Manager: portage-2.2.28
* sci-biology/samtools: Trim DESCRIPTIONDavid Seifert2016-03-281-3/+3
| | | | | | * Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
* sci-biology/samtools: Trim DESCRIPTIONDavid Seifert2016-03-281-3/+3
| | | | | | * Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
* sci-biology/samtools: Trim DESCRIPTIONDavid Seifert2016-03-281-3/+3
| | | | | | * Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
* sci-biology/samtools: Trim DESCRIPTIONDavid Seifert2016-03-281-3/+3
| | | | | | * Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
* sci-biology/samtools: Trim DESCRIPTIONDavid Seifert2016-03-281-3/+3
| | | | | | * Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
* sci-biology/samtools: Trim DESCRIPTIONDavid Seifert2016-03-281-2/+2
| | | | Package-Manager: portage-2.2.28
* sci-biology/biopython: Add python3_5 supportDavid Seifert2016-03-271-2/+2
| | | | Package-Manager: portage-2.2.28
* sci-biology/bioruby: Remove ruby19Manuel Rüger2016-03-202-4/+4
| | | | Package-Manager: portage-2.2.28
* sci-biology/seaview: ppc stable wrt bug #575914Agostino Sarubbo2016-03-161-1/+1
| | | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/primer3: ppc stable wrt bug #575016Agostino Sarubbo2016-03-161-1/+1
| | | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/seaview: x86 stable wrt bug #575914Agostino Sarubbo2016-03-151-1/+1
| | | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/primer3: x86 stable wrt bug #575016Agostino Sarubbo2016-03-151-1/+1
| | | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/phrap: Fix dependency on dev-perl/TkKent Fredric2016-03-151-2/+2
| | | | Package-Manager: portage-2.2.27
* sci-biology/biojava: Remove outdated unmaintained packageJames Le Cuirot2016-03-064-160/+0
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* sci-biology/mauvealigner: Remove outdated unmaintained packageJames Le Cuirot2016-03-062-43/+0
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* sci-biology/mauve: Remove outdated unmaintained packageJames Le Cuirot2016-03-062-62/+0
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* sci-biology/seaview: amd64 stable wrt bug #575914Agostino Sarubbo2016-03-061-1/+1
| | | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/primer3: amd64 stable wrt bug #575016Agostino Sarubbo2016-03-061-1/+1
| | | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/primer3: Version BumpJustin Lecher2016-02-182-0/+49
| | | | | Package-Manager: portage-2.2.27 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Drop oldJustin Lecher2016-02-143-94/+0
| | | | | Package-Manager: portage-2.2.27 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: amd64/ppc/x86 stable, (ALLARCHES policy) wrt bug #573576Agostino Sarubbo2016-02-131-1/+1
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/abyss: fix automagic haskell deps, bug #534412Sergei Trofimovich2016-02-082-4/+22
| | | | | | | Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/534412 Package-Manager: portage-2.2.27
* sci-biology/mira: Add missing <sys-devel/flex-2.6.0 dependencyDavid Seifert2016-02-082-2/+14
| | | | | | | | Gentoo-Bug: 574172 * Fix GCC5 explicit conversion of 'nullptr' to 'bool' * Fix overlong DESCRIPTION Package-Manager: portage-2.2.27