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* sci-biology/phyml: [QA] Consistent whitespace in metadata.xmlDavid Seifert2017-11-251-9/+9
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* sci-biology/njplot: [QA] Consistent whitespace in metadata.xmlDavid Seifert2017-11-251-5/+5
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* sci-biology/mcl: [QA] Consistent whitespace in metadata.xmlDavid Seifert2017-11-251-9/+7
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* sci-biology/fasttree: [QA] Consistent whitespace in metadata.xmlDavid Seifert2017-11-251-10/+10
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* sci-biology/exonerate: [QA] Consistent whitespace in metadata.xmlDavid Seifert2017-11-251-8/+8
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* sci-biology/emboss: [QA] Consistent whitespace in metadata.xmlDavid Seifert2017-11-251-8/+8
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* sci-biology/cutg: [QA] Consistent whitespace in metadata.xmlDavid Seifert2017-11-251-5/+5
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* sci-biology/arb: Version bump to 6.0.6Peter Levine2017-11-185-0/+273
| | | | | | Closes: https://bugs.gentoo.org/637118 Package-Manager: Portage-2.3.10, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5942
* sci-biology/kallisto: Initial additionDavid Seifert2017-11-164-0/+70
| | | | | Closes: https://github.com/gentoo/sci/pull/814 Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/STAR: Initial additionDavid Seifert2017-11-164-0/+185
| | | | | Closes: https://github.com/gentoo/sci/pull/814 Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/HTSeq: Initial additionDavid Seifert2017-11-164-0/+82
| | | | | Closes: https://github.com/gentoo/sci/pull/814 Package-Manager: Portage-2.3.14, Repoman-2.3.6
* 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