Commit message (Collapse) | Author | Age | Files | Lines | |
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* | sci-biology/mcl: [QA] Consistent whitespace in metadata.xml | David Seifert | 2017-11-25 | 1 | -9/+7 |
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* | sci-biology/fasttree: [QA] Consistent whitespace in metadata.xml | David Seifert | 2017-11-25 | 1 | -10/+10 |
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* | sci-biology/exonerate: [QA] Consistent whitespace in metadata.xml | David Seifert | 2017-11-25 | 1 | -8/+8 |
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* | sci-biology/emboss: [QA] Consistent whitespace in metadata.xml | David Seifert | 2017-11-25 | 1 | -8/+8 |
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* | sci-biology/cutg: [QA] Consistent whitespace in metadata.xml | David Seifert | 2017-11-25 | 1 | -5/+5 |
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* | sci-biology/arb: Version bump to 6.0.6 | Peter Levine | 2017-11-18 | 5 | -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 addition | David Seifert | 2017-11-16 | 4 | -0/+70 |
| | | | | | Closes: https://github.com/gentoo/sci/pull/814 Package-Manager: Portage-2.3.14, Repoman-2.3.6 | ||||
* | sci-biology/STAR: Initial addition | David Seifert | 2017-11-16 | 4 | -0/+185 |
| | | | | | Closes: https://github.com/gentoo/sci/pull/814 Package-Manager: Portage-2.3.14, Repoman-2.3.6 | ||||
* | sci-biology/HTSeq: Initial addition | David Seifert | 2017-11-16 | 4 | -0/+82 |
| | | | | | Closes: https://github.com/gentoo/sci/pull/814 Package-Manager: Portage-2.3.14, Repoman-2.3.6 | ||||
* | sci-biology/bamtools: Minor fixes | David Seifert | 2017-11-02 | 2 | -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 old | David Seifert | 2017-11-02 | 4 | -313/+0 |
| | | | | Package-Manager: Portage-2.3.11, Repoman-2.3.3 | ||||
* | sci-biology/bamtools: Add live ebuild | David Seifert | 2017-11-02 | 1 | -0/+27 |
| | | | | Package-Manager: Portage-2.3.11, Repoman-2.3.3 | ||||
* | sci-biology/bamtools: Version bump to 2.4.2 | David Seifert | 2017-11-02 | 2 | -0/+28 |
| | | | | Package-Manager: Portage-2.3.11, Repoman-2.3.3 | ||||
* | sci-biology/trnascan-se: remove unused patches. | Michael Mair-Keimberger | 2017-10-27 | 2 | -318/+0 |
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* | sci-biology/psipred: remove unused patch. | Michael Mair-Keimberger | 2017-10-27 | 1 | -13/+0 |
| | | | | Closes: https://github.com/gentoo/gentoo/pull/5720 | ||||
* | sci-biology/gibbs: remove unused file. | Michael Mair-Keimberger | 2017-10-04 | 1 | -7/+0 |
| | | | | Closes: https://github.com/gentoo/gentoo/pull/5803 | ||||
* | sci-biology/fasta: Strip empty metadata.xml elements | Michał Górny | 2017-10-04 | 1 | -2/+0 |
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* | sci-biology/ApE: Strip empty metadata.xml elements | Michał Górny | 2017-10-04 | 1 | -2/+0 |
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* | sci-biology/eugene: remove 4.1 | Michael Palimaka | 2017-09-30 | 2 | -37/+0 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/eugene: stabilise 4.1d for amd64/x86 | Michael Palimaka | 2017-09-30 | 1 | -2/+2 |
| | | | | | Closes: https://bugs.gentoo.org/632358 Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/clustal-omega: remove 1.2.1/1.2.3 | Michael Palimaka | 2017-09-30 | 4 | -103/+0 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/clustal-omega: stabilise 1.2.4 for amd64/x86 | Michael Palimaka | 2017-09-30 | 1 | -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 #421799 | Kent Fredric | 2017-09-26 | 1 | -52/+0 |
| | | | | | Closes: https://bugs.gentoo.org/421799 Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/hmmer: de-stabilize | Kent Fredric | 2017-09-26 | 1 | -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 Arahesis | 2017-09-22 | 2 | -2/+2 |
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* | sci-biology/goby: Depend directly on dev-java/protobuf-java. | Arfrever Frehtes Taifersar Arahesis | 2017-09-21 | 2 | -4/+4 |
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* | sci-biology/foldingathome: drop old 7.4.4-r1 ebuild | Ian Stakenvicius | 2017-09-21 | 3 | -122/+0 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.1 | ||||
* | sci-biology/foldingathome: minor ebuild improvements | Ian Stakenvicius | 2017-09-21 | 1 | -5/+5 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.1 | ||||
* | sci-biology/foldingathome: misc ebuild impovements | Ian Stakenvicius | 2017-09-20 | 1 | -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 old | David Seifert | 2017-09-17 | 2 | -48/+0 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/pysam: Version bump to 0.12.0.1 | David Seifert | 2017-09-17 | 2 | -0/+48 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/cufflinks: Fix boost TR1 header include | David Seifert | 2017-09-16 | 2 | -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 -I | David Seifert | 2017-09-02 | 2 | -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 CPPFLAGS | David Seifert | 2017-09-02 | 1 | -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 path | Francesco Turco | 2017-09-03 | 1 | -2/+2 |
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* | sci-biology/samtools: Remove old | David Seifert | 2017-09-02 | 14 | -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 old | David Seifert | 2017-09-02 | 3 | -86/+0 |
| | | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593 | ||||
* | sci-biology/bwa: Remove old | David Seifert | 2017-09-02 | 4 | -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 overlay | David Seifert | 2017-09-02 | 5 | -0/+95 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/pysam: Bump to 0.12 | David Seifert | 2017-09-02 | 2 | -0/+44 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/samtools: Version bump to 1.5 | David Seifert | 2017-09-02 | 3 | -0/+475 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/bwa: Bump to 0.7.16a | David Seifert | 2017-09-02 | 2 | -0/+35 |
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 | ||||
* | sci-biology/bioruby: remove obsolete live ebuild; add ruby22 | Hans de Graaff | 2017-08-20 | 2 | -40/+1 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 | ||||
* | media-gfx/pydot: move to dev-python/pydot | Tim Harder | 2017-08-19 | 1 | -1/+1 |
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* | sci-biology/bioruby: add 1.5.1 | Hans de Graaff | 2017-08-15 | 2 | -0/+23 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 | ||||
* | sci-biology/bioperl-run: use HTTPS for GitHub | David Hicks | 2017-07-30 | 1 | -3/+2 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3 | ||||
* | sci-biology/bioruby: use HTTPS for GitHub, update SRC_URI and HOMEPAGE | David Hicks | 2017-07-30 | 2 | -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 GitHub | David Hicks | 2017-07-30 | 1 | -3/+2 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3 | ||||
* | sci-biology/bioperl: use HTTPS for GitHub | David Hicks | 2017-07-30 | 1 | -3/+2 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3 | ||||
* | sci-biology/bioperl-network: use HTTPS for GitHub | David Hicks | 2017-07-30 | 1 | -3/+2 |
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3 |