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* 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
* sci-biology/blat: Modernise to EAPI 6David Seifert2017-03-082-0/+249
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/elph: Remove oldDavid Seifert2017-03-084-197/+0
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/iqpnni: Remove oldDavid Seifert2017-03-083-47/+0
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/mummer: Remove oldDavid Seifert2017-03-088-342/+0
| | | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/mummer: Version bump to 3.23David Seifert2017-03-085-0/+602
| | | | | | | | | * EAPI 6 * Make build system saner * Fix C++ QA warnings Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
* sci-biology/prints: Modernise to EAPI 6David Seifert2017-03-081-12/+14
| | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2
* sci-biology/elph: Modernise to EAPI 6David Seifert2017-03-082-0/+86
| | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2
* sci-biology/biosql: Modernise to EAPI 6David Seifert2017-03-081-11/+22
| | | | Package-Manager: Portage-2.3.4, Repoman-2.3.2
* Drop $Id$ per council decision in bug #611234.Robin H. Johnson2017-02-28215-215/+0
| | | | Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2017-02-272-0/+47
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/ariadne: Remove oldDavid Seifert2017-02-262-78/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/ariadne: Modernise to EAPI 6David Seifert2017-02-262-2/+49
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/snpfile: Remove oldDavid Seifert2017-02-262-62/+0
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/4083
* sci-biology/snpfile: Modernise to EAPI 6David Seifert2017-02-263-4/+86
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/4083
* sci-biology/blossoc: Remove oldDavid Seifert2017-02-261-31/+0
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/4083
* sci-biology/blossoc: Modernise to EAPI 6David Seifert2017-02-263-2/+295
| | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 RepoMan-Options: --force Closes: https://github.com/gentoo/gentoo/pull/4083
* sci-biology/prodigal: Remove oldDavid Seifert2017-02-253-62/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/prodigal: Version bump to 2.6.3David Seifert2017-02-253-0/+73
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/njplot: Remove oldDavid Seifert2017-02-252-69/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/njplot: Modernise to EAPI 6David Seifert2017-02-251-0/+39
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/sim4: Remove oldDavid Seifert2017-02-252-45/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1