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* sci-biology/bamtools: Minor fixesDavid Seifert2017-11-022-2/+18
| | | | | | | * Add 'virtual/pkgconfig' to DEPEND * Delete bundled libs for safety Package-Manager: Portage-2.3.11, Repoman-2.3.3
* sci-biology/bamtools: Remove oldDavid Seifert2017-11-024-313/+0
| | | | Package-Manager: Portage-2.3.11, Repoman-2.3.3
* sci-biology/bamtools: Add live ebuildDavid Seifert2017-11-021-0/+27
| | | | Package-Manager: Portage-2.3.11, Repoman-2.3.3
* sci-biology/bamtools: Version bump to 2.4.2David Seifert2017-11-022-0/+28
| | | | Package-Manager: Portage-2.3.11, Repoman-2.3.3
* sci-biology/trnascan-se: remove unused patches.Michael Mair-Keimberger2017-10-272-318/+0
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* sci-biology/psipred: remove unused patch.Michael Mair-Keimberger2017-10-271-13/+0
| | | | Closes: https://github.com/gentoo/gentoo/pull/5720
* sci-biology/gibbs: remove unused file.Michael Mair-Keimberger2017-10-041-7/+0
| | | | Closes: https://github.com/gentoo/gentoo/pull/5803
* sci-biology/fasta: Strip empty metadata.xml elementsMichał Górny2017-10-041-2/+0
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* sci-biology/ApE: Strip empty metadata.xml elementsMichał Górny2017-10-041-2/+0
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* sci-biology/eugene: remove 4.1Michael Palimaka2017-09-302-37/+0
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/eugene: stabilise 4.1d for amd64/x86Michael Palimaka2017-09-301-2/+2
| | | | | Closes: https://bugs.gentoo.org/632358 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/clustal-omega: remove 1.2.1/1.2.3Michael Palimaka2017-09-304-103/+0
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/clustal-omega: stabilise 1.2.4 for amd64/x86Michael Palimaka2017-09-301-2/+2
| | | | | Closes: https://bugs.gentoo.org/632344 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/hmmer: Cleanup broken versions re bug #421799Kent Fredric2017-09-261-52/+0
| | | | | Closes: https://bugs.gentoo.org/421799 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/hmmer: de-stabilizeKent Fredric2017-09-261-1/+1
| | | | | | | | | Sci Team don't want unnecessary stable pacakges, and this is not necessary. The stated stable versions are broken on all available perls anyway. Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/goby: Fix path to protobuf-java in EANT_GENTOO_CLASSPATH.Arfrever Frehtes Taifersar Arahesis2017-09-222-2/+2
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* sci-biology/goby: Depend directly on dev-java/protobuf-java.Arfrever Frehtes Taifersar Arahesis2017-09-212-4/+4
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* sci-biology/foldingathome: drop old 7.4.4-r1 ebuildIan Stakenvicius2017-09-213-122/+0
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.1
* sci-biology/foldingathome: minor ebuild improvementsIan Stakenvicius2017-09-211-5/+5
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.1
* sci-biology/foldingathome: misc ebuild impovementsIan Stakenvicius2017-09-201-0/+126
| | | | | | | | | | - Added a systemd unit - Removed usage of 'chown -R' on live filesystems - Dropped the custom and vulnerable 'initfolding' helper script - Improved the init script to use standard openrc-run behaviour via variables - Dropped "unitinfo" extra command on /etc/init.d/foldingathome as it rarely works Package-Manager: Portage-2.3.6, Repoman-2.3.1
* sci-biology/pysam: Remove oldDavid Seifert2017-09-172-48/+0
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/pysam: Version bump to 0.12.0.1David Seifert2017-09-172-0/+48
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/cufflinks: Fix boost TR1 header includeDavid Seifert2017-09-162-10/+39
| | | | | | | * Also fix missing python dependencies Closes: https://bugs.gentoo.org/630654 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* 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>