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* 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
* sci-biology/rebase: Version BumpJustin Lecher2016-02-012-0/+47
| | | | | Package-Manager: portage-2.2.27 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Set appropriate maintainer types in metadata.xml (GLEP 67)Michał Górny2016-01-24151-161/+161
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* Replace all herds with appropriate projects (GLEP 67)Michał Górny2016-01-24150-153/+612
| | | | | Replace all uses of herd with appropriate project maintainers, or no maintainers in case of herds requested to be disbanded.
* Unify quoting in metadata.xml files for machine processingMichał Górny2016-01-2421-22/+21
| | | | | | | Force unified quoting in all metadata.xml files since lxml does not preserve original use of single and double quotes. Ensuring unified quoting before the process allows distinguishing the GLEP 67-related metadata.xml changes from unrelated quoting changes.
* sci-biology/iedera: Remove hardcoded {C,CXX,LD}FLAGS from configure.acDavid Seifert2016-01-212-4/+24
| | | | Package-Manager: portage-2.2.27
* sci-biology/gmap: Version bump to 2015.12.31.5David Seifert2016-01-212-0/+22
| | | | | | | | Gentoo-Bug: 521640 * Remove use of 'einstall' * EAPI=6 Package-Manager: portage-2.2.27
* Fix typo repo wideJustin Lecher2016-01-211-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/iedera: Version bump to 1.05David Seifert2016-01-212-0/+23
| | | | | | | | Gentoo-Bug: 521642 * Remove use of 'einstall' * EAPI=6 Package-Manager: portage-2.2.26
* sci-biology/newick-utils: Version bump to 1.6David Seifert2016-01-212-0/+22
| | | | | | | | Gentoo-Bug: 521644 * Remove use of 'einstall' * EAPI=6 Package-Manager: portage-2.2.26
* sci-biology/vaal: Place blockers on sci-biology/allpaths{,lg}David Seifert2016-01-171-4/+10
| | | | | | Gentoo-Bug: 572128 Package-Manager: portage-2.2.26
* sci-biology/allpathslg: Add blocking packages to RDEPEND tooDavid Seifert2016-01-171-6/+10
| | | | Package-Manager: portage-2.2.26
* Drop myself as maintainerJustin Lecher2016-01-093-10/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Update remote-ids in metadata.xmlJustin Lecher2016-01-071-1/+2
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Drop oldJustin Lecher2016-01-032-47/+0
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: amd64/ppc/x86 stable, (ALLARCHES policy) wrt bug #570636Agostino Sarubbo2016-01-021-1/+1
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/rebase: Drop oldJustin Lecher2016-01-022-47/+0
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2016-01-022-0/+47
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/dialign-tx: fixes GCC-5 inline semantics and -Wformat= warnings, ↵Ted Tanberry2015-12-312-1/+132
| | | | | | #570252 Package-Manager: portage-2.2.26
* sci-biology/allpathslg: Block sci-biology/vaal as it is nicluded in this releaseJustin Lecher2015-12-291-1/+1
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=570070 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/vaal: Remove old patchesTed Tanberry2015-12-275-286/+0
| | | | Package-Manager: portage-2.2.26