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* app-admin/eselect: Version BumpJustin Lecher2016-12-103-1/+1
| | | | | Package-Manager: portage-2.3.3 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/gsl: Version BumpJustin Lecher2016-12-103-0/+1565
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=602200 Package-Manager: portage-2.3.3 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/kat: respect sse CPU USE flagsMartin Mokrejš2016-12-091-3/+7
| | | | Package-Manager: portage-2.3.3
* sci-biology/kat:Martin Mokrejš2016-12-091-6/+14
| | | | Package-Manager: portage-2.3.3
* sci-biology/jellyfish: version bump; respect sse CPU USE flagMartin Mokrejš2016-12-095-3/+81
| | | | Package-Manager: portage-2.3.3
* sci-biology/freebayes: fix package herd nameMartin Mokrejš2016-12-091-2/+2
| | | | Package-Manager: portage-2.3.3
* sci-biology/grass: introduce -9999 live version, drop oldMartin Mokrejš2016-12-074-43/+309
| | | | | | fix the build system (https://github.com/AlexeyG/GRASS/issues/6) Package-Manager: portage-2.3.2
* sci-biology/trinityrnaseq: upstream removes fasta_tool script in future versionsMartin Mokrejš2016-12-071-0/+1
| | | | Package-Manager: portage-2.3.2
* dev-perl/Bio-DB-HTS: remove trailing empty lineMartin Mokrejš2016-12-071-1/+0
| | | | Package-Manager: portage-2.3.2
* dev-perl/Bio-DB-HTS: new package requiring sci-libs/[static-libs] and using ↵Martin Mokrejš2016-12-071-6/+13
| | | | | | -rpath Package-Manager: portage-2.3.2
* sci-biology/annovar: new packageMartin Mokrejš2016-12-073-0/+52
| | | | Package-Manager: portage-2.3.2
* sci-biology/ensembl-tools: mimic upstream's INSTALL.pl so we can install on ↵Martin Mokrejš2016-12-071-15/+22
| | | | | | | | | Gentoo Seems the code fetching VEP plugins will need more reverse-engineering unless this can be completed during run-time (do not know). Package-Manager: portage-2.3.2
* sci-biology/SnpEff: fix installation on PREFIXMartin Mokrejš2016-12-071-6/+6
| | | | Package-Manager: portage-2.3.2
* sci-biology/SnpEff: version bump, may be moved to our main repoMartin Mokrejš2016-12-072-8/+10
| | | | Package-Manager: portage-2.3.2
* Merge branch 'master' of ssh://github.com/gentoo-science/sciChristoph Junghans2016-12-062-0/+51
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| * sci-biology/psychopy: version bump (#706)Horea Christian2016-12-032-0/+51
| | | | | | Package-Manager: portage-2.3.2
* | sci-libs/trilinos: version bumpChristoph Junghans2016-12-063-0/+814
| | | | | | | | Package-Manager: portage-2.3.0
* | sci-biology/jannovar-bin: version bumpMartin Mokrejš2016-12-043-32/+43
| | | | | | | | | | | | | | | | Provided sci-biology/jannovar download through maven lots of dependencies and anyway uses plenty of upstream jar file this sci-biology/jannovar-bin package is probably better choice due to size of downloads and security Package-Manager: portage-2.3.2
* | sci-biology/jannovar: version bump, seems only one jar can be directly executedMartin Mokrejš2016-12-042-16/+12
| | | | | | | | | | | | | | https://github.com/charite/jannovar/issues/218 https://github.com/charite/jannovar/releases Package-Manager: portage-2.3.2
* | sci-biology/plinkseq: fixing issues with bundled dev-libs/protobuf and ↵Martin Mokrejš2016-12-042-3/+64
| | | | | | | | | | | | | | | | | | | | | | | | www-servers/mongoose The git repo received some commits this year so trying to create an ebuild for that. It bailed out at more places than the latest release tarball v0.10. The static Makefile needs more tweaks so that the values from 'pkg-config protobuf' calls get propagated properly. And not to look for the removed protobuf and mongoose subdirs. Package-Manager: portage-2.3.2
* | sci-biology/BRAKER: version bump, point to additional dependencyMartin Mokrejš2016-12-032-4/+3
| | | | | | | | Package-Manager: portage-2.3.2
* | sci-biology/maker: record required augustus version actuallyMartin Mokrejš2016-12-031-1/+4
| | | | | | | | Package-Manager: portage-2.3.2
* | sci-biology/ncbi-tools++: add a comment about >=gcc-5.3.0 incompatibilityMartin Mokrejš2016-12-031-0/+3
| | | | | | | | Package-Manager: portage-2.3.2
* | sci-biology/ncbi-tools++: fix bug #579248#c by disabling more testsMartin Mokrejš2016-12-033-0/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This will likely also fix the #579248 bug in rmblast (untested). Our $FILESDIR/disable-testsuite-compilation.txt only excludes test applications from usingboost, not the support library. Hence the above bug. We could either add --without-boost to the configuration command line to disable the bosost-related code in support library or, which is the path we take in this commit, we disable building of the yet escaping unit_tests which needed boost. Upstream further said: The C++ Toolkit makes very little use of Boost outside of unit tests, but that's a fair question. The simplest fix preserving other uses of Boost would be to edit .../src/corelib/Makefile.in and remove test_boost from LIB_PROJ. (You'll still also need to exclude building the tests by adding '-.*/unit_tests' to the $FILESDIR/disable-testsuite-compilation.txt file.) Package-Manager: portage-2.3.2
* | sci-biology/ensembl-tools: add missing dependencyMartin Mokrejš2016-12-021-3/+2
| | | | | | | | Package-Manager: portage-2.3.2
* | dev-perl/Bio-EnsEMBL: new package to provide EnsEMBL Perl APIMartin Mokrejš2016-12-023-0/+48
| | | | | | | | | | | | | | | | This is needed by sci-biology/ensembl-tools, do not miss the official installation procedure at http://www.ensembl.org/info/docs/api/api_installation.html Package-Manager: portage-2.3.2
* | sci-biology/freebayes: note the many bundled deps we need to unbundleMartin Mokrejš2016-12-021-0/+64
| | | | | | | | Package-Manager: portage-2.3.2
* | sci-biology/ensembl-tools: note dependency not yet in science overlayMartin Mokrejš2016-12-022-3/+5
| | | | | | | | Package-Manager: portage-2.3.2
* | sci-biology/stacks: add missing dependencyMartin Mokrejš2016-12-021-1/+2
|/ | | | Package-Manager: portage-2.3.2
* sci-libs/atlas-3.10.3: Add deprecated use flagMarius Brehler2016-12-021-3/+8
| | | | Package-Manager: portage-2.3.0
* sci-biology/augustus: zap -O3 CFLAG from src/MakefileMartin Mokrejš2016-12-011-1/+2
| | | | Package-Manager: portage-2.3.2
* sci-biology/gmap: version bump; drop unused USE flags from metadata.xmlMartin Mokrejš2016-12-013-0/+32
| | | | Package-Manager: portage-2.3.2
* sci-biology/stacks: version bump; drop bundled htslib sources, bug #601366Martin Mokrejš2016-12-012-6/+14
| | | | Package-Manager: portage-2.3.2
* sci-biology/trinityrnaseq: do not install fasta_tool which belongs to ↵Martin Mokrejš2016-12-013-3/+3
| | | | | | sci-biology/GAL Package-Manager: portage-2.3.2
* sci-biology/twinscan: add missing space breaking GLIB_CFLAGSMartin Mokrejš2016-12-011-1/+1
| | | | Package-Manager: portage-2.3.2
* sci-libs/arrayfire: Fix FindCBLAS.cmake in 3.4.1-r1Marius Brehler2016-12-012-0/+39
| | | | Package-Manager: portage-2.3.0
* sci-biology/kat: version bump, blocked by upstream issue #61Martin Mokrejš2016-11-302-3/+9
| | | | Package-Manager: portage-2.3.2
* dev-python/arrayfire-python: Add test phaseMarius Brehler2016-11-291-0/+5
| | | | Package-Manager: portage-2.3.0
* dev-python/arrayfire-python: Version bump to 3.4.20161126Marius Brehler2016-11-292-0/+23
| | | | Package-Manager: portage-2.3.0
* sci-libs/arrayfire: Version bump to 3.4.1Marius Brehler2016-11-292-0/+112
| | | | Package-Manager: portage-2.3.0
* dev-python/arrayfire-python: Drop oldMarius Brehler2016-11-292-23/+0
| | | | Package-Manager: portage-2.3.0
* dev-python/arrayfire-python: Drop python3_3Marius Brehler2016-11-295-5/+5
| | | | Package-Manager: portage-2.3.0
* dev-python/arrayfire-python: Restrict package to corresponding arrayfire versionMarius Brehler2016-11-294-0/+4
| | | | Package-Manager: portage-2.3.0
* dev-python/arrayfire-python: Version bump to 3.3.20160624Marius Brehler2016-11-292-0/+22
| | | | Package-Manager: portage-2.3.0
* sci-chemistry/gamess: Update install infoAlexey Shvetsov2016-11-291-0/+4
| | | | Package-Manager: portage-2.3.0
* sci-chemistry/gamess: Update gamess version. Clean old onesAlexey Shvetsov2016-11-295-589/+43
| | | | Package-Manager: portage-2.3.0
* sci-libs/pydicom: Drop 0.9.8Marius Brehler2016-11-282-19/+0
| | | | Package-Manager: portage-2.3.0
* sci-libs/bloom: Move SRC_URI from google code to github; Fix compilationMarius Brehler2016-11-281-5/+5
| | | | | | Still broken, since the Makefile provides no install phase Package-Manager: portage-2.3.0
* sci-misc/mitlm: Move SRC_URI from google code to githubMarius Brehler2016-11-281-3/+3
| | | | Package-Manager: portage-2.3.0
* licenses: Add MIT-KhronosGroup licenseMarius Brehler2016-11-281-0/+25
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