Get Gentoo!
gentoo.org sites
gentoo.org Wiki Bugs Forums Packages
Planet Archives Sources
Infra Status
summaryrefslogtreecommitdiff
path: root/sci-biology
Commit message (Collapse)AuthorAgeFilesLines
* sci-biology/shrimp: Remove oldDavid Seifert2019-12-112-55/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/velvet: Port to EAPI 7David Seifert2019-12-113-126/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/augustus: Port to EAPI 7David Seifert2019-12-111-9/+10
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/tree-puzzle: Port to EAPI 7David Seifert2019-12-111-21/+18
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mrbayes: Remove oldDavid Seifert2019-12-111-51/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/plink: Remove oldDavid Seifert2019-12-115-164/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/last: Remove oldDavid Seifert2019-12-112-40/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gibbs: Port to EAPI 7David Seifert2019-12-112-18/+27
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/glimmerhmm: Port to EAPI 7David Seifert2019-12-112-17/+34
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* */*: [QA] Fix trivial cases of MissingTestRestrictMichał Górny2019-12-1113-11/+24
| | | | | | | | | | | | | | | | | | The result was achieved via the following pipeline: pkgcheck scan -c RestrictTestCheck -R FormatReporter \ --format '{category}/{package}/{package}-{version}.ebuild' | xargs -n32 grep -L RESTRICT | xargs -n32 sed -i -e '/^IUSE=.*test/aRESTRICT="!test? ( test )"' The resulting metadata was compared before and after the change. Few Go ebuilds had to be fixed manually due to implicit RESTRICT=strip added by the eclass. Two ebuilds have to be fixed because of multiline IUSE. Suggested-by: Robin H. Johnson <robbat2@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/13942 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/mcl: drop old EAPIAaron Bauman2019-11-233-74/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/psipred: drop old EAPIAaron Bauman2019-11-233-107/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/ariadne: drop last-rited packageAaron Bauman2019-11-205-100/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/bamtools: Remove USE="static-libs"David Seifert2019-11-132-60/+6
| | | | | Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/goby-cpp: Remove last-rited pkgMichał Górny2019-10-145-104/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: Remove mirror://gentoo rename hackMichał Górny2019-10-051-1/+1
| | | | | | | | Replace 'mirror://gentoo/X -> Y' with plain 'mirror://gentoo/Y'. Since actual filenames are used on the mirrors, the latter is valid for all packages already. Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/ApE: Add bindist restrictionMichał Górny2019-09-191-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* Make a bunch of metadata.xml files uniformMatt Turner2019-09-151-1/+1
| | | | | | When put into a squashfs image, these files are deduplicated. Signed-off-by: Matt Turner <mattst88@gentoo.org>
* sci-biology/goby: Remove last-rited pkgMichał Górny2019-09-144-127/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioruby: amd64 stable wrt bug #690048Agostino Sarubbo2019-09-081-1/+1
| | | | | | Package-Manager: Portage-2.3.69, Repoman-2.3.16 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bioruby: x86 stable (bug #690048)Thomas Deutschmann2019-09-071-1/+1
| | | | | Package-Manager: Portage-2.3.75, Repoman-2.3.17 Signed-off-by: Thomas Deutschmann <whissi@gentoo.org>
* sci-biology/stride: Port to EAPI 7David Seifert2019-08-173-25/+31
| | | | | Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/stride: [QA] Version the distfileDavid Seifert2019-08-172-3/+3
| | | | | Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/sim4: [QA] Version the distfileDavid Seifert2019-08-172-4/+4
| | | | | Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/vaal: remove last rited packageMikle Kolyada2019-07-224-72/+0
| | | | Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
* sci-biology/allpathslg: remove last rited packageMikle Kolyada2019-07-224-69/+0
| | | | Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
* */*: Add maintainer-needed comment to all unmaintained packagesMichał Górny2019-07-171-0/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/vcftools: Sort KEYWORDSMichał Górny2019-07-151-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/poa: Sort KEYWORDSMichał Górny2019-07-151-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bedtools: Sort KEYWORDSMichał Górny2019-07-151-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/foldingathome: Permit dev-libs/openssl-compatMichał Górny2019-06-141-1/+4
| | | | | Signed-off-by: Michał Górny <mgorny@gentoo.org> Signed-off-by: Thomas Deutschmann <whissi@gentoo.org>
* sci-biology/{blossoc,snpfile}: Remove last-rited pkgsDavid Seifert2019-05-1912-974/+0
| | | | | Closes: https://bugs.gentoo.org/683762 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/cufflinks: Remove last-rited pkgDavid Seifert2019-05-1910-314/+0
| | | | | Closes: https://bugs.gentoo.org/671432 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/arb: remove last rited packageMikle Kolyada2019-05-026-281/+0
| | | | Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
* sci-biology/biopython: Bump to version 1.73David Seifert2019-04-212-0/+59
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: David Seifert <soap@gentoo.org>
* */*: Remove python3_4 PYTHON_COMPAT correctlyMichał Górny2019-04-176-12/+12
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: Drop python3_4 from PYTHON_COMPATMichał Górny2019-04-161-1/+1
| | | | | Closes: https://github.com/gentoo/gentoo/pull/11706 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/consed: Fix building under GCC 7+David Seifert2019-04-062-1/+20
| | | | | | | | | | | consed (and MOTIF programs in general) is very sensitive to link order: * http://users.polytech.unice.fr/~buffa/cours/X11_Motif/motif-faq/part9/faq-doc-10.html * https://bugzilla.redhat.com/show_bug.cgi?id=870712 Closes: https://bugs.gentoo.org/681920 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bioruby: add 1.5.2Hans de Graaff2019-02-242-0/+23
| | | | | Signed-off-by: Hans de Graaff <graaff@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
* sci-biology/ucsc-genome-browser: Revbump to fix dependenciesBrian Evans2019-02-151-6/+8
| | | | | | | | | Non-maintainer commit Closes: https://bugs.gentoo.org/667578 Closes: https://bugs.gentoo.org/666050 Package-Manager: Portage-2.3.60, Repoman-2.3.12 Signed-off-by: Brian Evans <grknight@gentoo.org>
* sci-biology/phred: don't reference ${DISTDIR} in pkg_nofetchBen Kohler2019-02-051-2/+2
| | | | | Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Ben Kohler <bkohler@gentoo.org>
* sci-biology/phrap: don't reference ${DISTDIR} in pkg_nofetchBen Kohler2019-02-051-2/+2
| | | | | Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Ben Kohler <bkohler@gentoo.org>
* sci-biology/consed: don't reference ${DISTDIR} in pkg_nofetchBen Kohler2019-02-051-3/+3
| | | | | Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Ben Kohler <bkohler@gentoo.org>
* sci-biology/repeatmasker-libraries: don't reference ${DISTDIR}Ben Kohler2019-02-051-2/+2
| | | | | Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Ben Kohler <bkohler@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2018-12-312-0/+46
| | | | | Package-Manager: Portage-2.3.53, Repoman-2.3.12 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bamtools: Bump to EAPI 7David Seifert2018-12-132-32/+12
| | | | | Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: Version bump to 1.9David Seifert2018-10-283-0/+56
| | | | | | Closes: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert <soap@gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11
* sci-biology/samtools: Version bump to 1.9David Seifert2018-10-282-0/+53
| | | | | | Bug: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert <soap@gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11
* sci-biology/allpathslg: Fix build with glibc-2.27Pacho Ramos2018-10-211-1/+4
| | | | | | Closes: https://bugs.gentoo.org/647340 Signed-off-by: Pacho Ramos <pacho@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
* sci-biology/rebase: Version BumpJustin Lecher2018-10-212-0/+46
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.40, Repoman-2.3.9