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* sci-biology/pysam: Fix broken relative -IDavid Seifert2017-09-022-1/+68
| | | | | Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/samtools: Add missing -I. to CPPFLAGSDavid Seifert2017-09-021-1/+1
| | | | | Bug: https://bugs.gentoo.org/show_bug.cgi?id=629666 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/velvet: update make.conf pathFrancesco Turco2017-09-031-2/+2
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* sci-biology/samtools: Remove oldDavid Seifert2017-09-0214-1995/+0
| | | | | | | | Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170 Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618 Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504 Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593
* sci-biology/pysam: Remove oldDavid Seifert2017-09-023-86/+0
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593
* sci-biology/bwa: Remove oldDavid Seifert2017-09-024-98/+0
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593
* sci-biology/bcftools: Add 1.5 from sci overlayDavid Seifert2017-09-025-0/+95
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/pysam: Bump to 0.12David Seifert2017-09-022-0/+44
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/samtools: Version bump to 1.5David Seifert2017-09-023-0/+475
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/bwa: Bump to 0.7.16aDavid Seifert2017-09-022-0/+35
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/bioruby: remove obsolete live ebuild; add ruby22Hans de Graaff2017-08-202-40/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* media-gfx/pydot: move to dev-python/pydotTim Harder2017-08-191-1/+1
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* sci-biology/bioruby: add 1.5.1Hans de Graaff2017-08-152-0/+23
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/bioperl-run: use HTTPS for GitHubDavid Hicks2017-07-301-3/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/bioruby: use HTTPS for GitHub, update SRC_URI and HOMEPAGEDavid Hicks2017-07-302-5/+4
| | | | | | | | * Use HTTPS for accessing GitHub domains * Update SRC_URI and HOMEPAGE to remove "www" as this prefix is no longer used on the bioruby website Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/bioperl-db: use HTTPS for GitHubDavid Hicks2017-07-301-3/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/bioperl: use HTTPS for GitHubDavid Hicks2017-07-301-3/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/bioperl-network: use HTTPS for GitHubDavid Hicks2017-07-301-3/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/express: Fix building with GCC-6Peter Levine2017-07-302-1/+21
| | | | | | Bug: https://bugs.gentoo.org/show_bug.cgi?id=610692 Package-Manager: Portage-2.3.6, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/5179
* sci-biology/bioperl-db: Restrict tests re bug #421701Kent Fredric2017-07-183-46/+58
| | | | | | | | | | | | | | | | | I've tried an excessive amount to get tests working here. But they still need a lot of love. The work I've done so far only gets a mysql test instance up, ( and then, only tested with mariadb ) Somebody needs to work out what's missing to provision the databases that the tests use. Somebody needs to add support for initializing the other kinds of database. Any help here encouraged, but disabling non-functioning tests is the best we can do for now. Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/bioperl-db: EAPI6/-R1 BumpKent Fredric2017-07-182-0/+118
| | | | | | | | | - Test infa overhauled slightly - EAPI6ified - More test changes planned - -r1 bump mostly for double-safety around EAPI6 changes Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/bioperl-db: Fix broken test dependenciesKent Fredric2017-07-181-2/+15
| | | | | | | | | | | | | | Bundled versions of CPAN modules in t/ lacked all their dependencies being declared, leading to bundled copy of Test::Warn fail when Array::Compare was not installed. Additionally, parts didn't play nice together and warned about old versions of things. This is fixed buy uncermoniously removing all bundled test libraries and marking them as dependencies instead. Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/cufflinks: Fix building with GCC-6Peter Levine2017-06-252-1/+16
| | | | | | Bug: https://bugs.gentoo.org/show_bug.cgi?id=594904 Package-Manager: Portage-2.3.6, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4969
* sci-biology/mammoth: Remove last-rited pkg, #612738Michał Górny2017-06-154-72/+0
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* sci-biology/biopandas: Version BumpJustin Lecher2017-06-042-0/+43
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/mammoth: update homepageSergei Trofimovich2017-05-261-2/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* Globally add missing remote ID references to metadata.xmlJustin Lecher2017-04-297-9/+18
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/trnascan-se: Drop oldJustin Lecher2017-04-292-45/+0
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/trnascan-se: x86 stable wrt bug #615564Agostino Sarubbo2017-04-271-1/+1
| | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2017-04-232-0/+46
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/trnascan-se: amd64 stable wrt bug #615564Agostino Sarubbo2017-04-231-1/+1
| | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/velvet: v4 expose additional variables as described in manualMartin Mokrejš2017-04-221-4/+3
| | | | | | | | | Also move the -j1 argument values onto the emake line directly. Package-Manager: Portage-2.3.5, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4421 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/velvet: v3 expose additional variables as described in manualMartin Mokrejš2017-04-221-4/+4
| | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4421 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/velvet: simplify tests in ebuildMartin Mokrejš2017-04-221-6/+6
| | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4421 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/velvet: expose additional variables as described in manual and ↵Martin Mokrejš2017-04-221-4/+9
| | | | | | | | | needed at compile time Package-Manager: Portage-2.3.5, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4421 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/foldingathome: switch EPREFIX usages in pkg_* back to EROOTIan Stakenvicius2017-04-211-3/+3
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/foldingathome: bump EAPIIan Stakenvicius2017-04-211-11/+11
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/foldingathome: drop obsolete versionIan Stakenvicius2017-04-212-83/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/foldingathome: fix use of $PORTDIR in phase functionIan Stakenvicius2017-04-211-9/+15
| | | | | | Bug: http://bugs.gentoo.org/566402 Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/seqan: [QA] Add missing python metadata variablesDavid Seifert2017-04-202-16/+36
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/samtools: [QA] Add missing python metadata variablesDavid Seifert2017-04-206-18/+18
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/last: [QA] Add missing python metadata variablesDavid Seifert2017-04-203-21/+190
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/trnascan-se: Bump EAPI to 6Justin Lecher2017-04-141-7/+8
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/unafold: Remove old, bug 605728Andreas K. Hüttel2017-04-101-31/+0
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/tophat: Unbundle python modulesDavid Seifert2017-04-012-11/+50
| | | | | Bug: https://bugs.gentoo.org/show_bug.cgi?id=614370 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/pilercr: Modernise to EAPI 6David Seifert2017-03-083-30/+64
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/piler: Modernise to EAPI 6David Seifert2017-03-083-35/+72
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/pals: Modernise to EAPI 6David Seifert2017-03-082-8/+43
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/clustalw-mpi: Modernise to EAPI 6David Seifert2017-03-081-6/+10
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/blat: Remove oldDavid Seifert2017-03-083-303/+0
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165