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* sci-biology/bedops: new packageMartin Mokrejš2017-04-284-0/+176
| | | | | | | | The patch does not expand properly CXXFLAGS for some reason. The package conatains bundled zlib. bzip2 and other 3rd-party stuff. It compile statically at least some binaries. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/ncbi-blast+: version bumpMartin Mokrejš2017-04-282-3/+7
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* Merge branch 'master' of ssh://github.com/gentoo-science/sciChristoph Junghans2017-04-256-125/+225
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| * sci-misc/kaldi: Version bump (#747)Pavel Denisov2017-04-236-125/+225
| | | | | | | | | | | | Adopt the version scheme introduced by upstream Add double-precision USE flag Package-Manager: Portage-2.3.4, Repoman-2.3.2
* | sci-physics/quinoa: fix depsChristoph Junghans2017-04-251-1/+1
| | | | | | | | | | Fix quinoacomputing/buildenv#4 Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/barrnap: respect EPREFIXMartin Mokrejš2017-04-252-4/+4
|/ | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* dev-util/emscripten: version bump (#778)Harald Weiner2017-04-228-3/+5
| | | Package-manager: portage-2.3.3 repoman-2.3.2
* sci-libs/nipype: updted dependencies (#776)Horea Christian2017-04-221-2/+6
| | | | | | upstream (as of now) still insists that pytest should be available at runtime and explicitly checks Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/acml: fix licenseChristoph Junghans2017-04-211-2/+2
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* Merge branch 'master' of ssh://github.com/gentoo-science/sciChristoph Junghans2017-04-212-23/+23
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| * Merge pull request #777 from bryant1410/masterMarius Brehler2017-04-182-23/+23
| |\ | | | | | | Fix broken headings in Markdown files
| | * Fix broken Markdown headingsSantiago Castro2017-04-182-23/+23
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* | dev-util/mad-numdiff: added live versionChristoph Junghans2017-04-211-0/+25
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/barrnap: get satisfied by any SLOTMartin Mokrejš2017-04-202-4/+4
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/oncotator: add license fileMartin Mokrejš2017-04-201-0/+46
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* | dev-python/pyvcf: add license fileMartin Mokrejš2017-04-201-0/+46
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* | dev-python/pyvcf: add license fileMartin Mokrejš2017-04-201-2/+1
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/oncotator: add LICENSE, add KEYWORDSMartin Mokrejš2017-04-201-1/+1
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/oncotator: drop python3_5 until issue #364 is answeredMartin Mokrejš2017-04-201-1/+1
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/oncotator: add RESTRICT="fetch" due to issue #362Martin Mokrejš2017-04-201-0/+2
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/oncotator: new packageMartin Mokrejš2017-04-203-0/+47
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/gffutils: version bumpMartin Mokrejš2017-04-202-2/+2
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | dev-python/shove: new packageMartin Mokrejš2017-04-203-0/+33
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | dev-python/bcbio-gff: new packageMartin Mokrejš2017-04-203-0/+32
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | dev-python/ngslib: new packageMartin Mokrejš2017-04-203-0/+36
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | dev-python/pyvcf: new packageMartin Mokrejš2017-04-203-0/+36
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/vcftools: add a pre-release versionMartin Mokrejš2017-04-193-0/+47
| | | | | | | | | | | | Our build patch for 0.1.14 was accepted by upstream. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-libs/libmaus2: make configure to enable optional but highly wanted featuresMartin Mokrejš2017-04-181-3/+17
| | | | | | | | | | | | | | | | | | | | | | | | The configure by default has a number of features disables, and does not enable the option. It somehow does not even try to look for headers and libs from say snappy unless --enable-snappy was passed. Try to blindly enable most of the features although it is not clear whether say gnutls should be preferred over nettle, likewise when --enable-sse4 is any better --enable-sse3 (and should not be enabled concurrently with it). Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/flexbar: version bump, added KEYWORDSMartin Mokrejš2017-04-152-0/+42
| | | | | | | | | | | | We still could filter away '-Wl,-O1' from CXXFLAGS. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-libs/io_lib: version bump, support for alternative zlib implementationsMartin Mokrejš2017-04-152-0/+29
|/ | | | | | | | | | It is not enabled in the ebuild but the sources are ready to links against a different implementation CloudFlare: https://github.com/cloudflare/zlib Intel: https://github.com/jtkukunas/zlib Zlib-ng: https://github.com/Dead2/zlib-ng Package-Manager: Portage-2.3.5, Repoman-2.3.2
* Update local USE descriptionJustin Lecher2017-04-141-0/+4
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* dev-python/py2bit: Drop Stale CVS headerJustin Lecher2017-04-141-1/+1
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/VarScan: add RDEPEND on bam-readcountMartin Mokrejš2017-04-142-3/+5
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/bam-readcount: new packageMartin Mokrejš2017-04-144-0/+49
| | | | | | Is needed by VarScan. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* Merge remote-tracking branch 'github/master'Justin Lecher2017-04-143-0/+43
|\ | | | | | | | | | | * github/master: added CeCILL-B license to MISC-FREE license group (#775) sci-visualization/mricrogl: version bump (#773)
| * added CeCILL-B license to MISC-FREE license group (#775)Alessandro Barbieri2017-04-141-0/+1
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| * sci-visualization/mricrogl: version bump (#773)Horea Christian2017-04-122-0/+42
| | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* | sci-biology/nxtrim: drop patch accepted by upstream nowMartin Mokrejš2017-04-122-48/+0
|/ | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* dev-util/f90cache: version bumpChristoph Junghans2017-04-112-0/+38
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/arrayfire: Apply upstream patch to 3.4.2Marius Brehler2017-04-112-0/+36
| | | | | | | Build fix for CUDA Compile PTX generated names by CMake 3.7 See https://github.com/arrayfire/arrayfire/issues/1755 Package-Manager: Portage-2.3.3, Repoman-2.3.1
* Merge remote-tracking branch 'github/master'Marius Brehler2017-04-1119-44/+372
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| * sci-libs/dealii: do not compile examplesMatthias Maier2017-04-071-0/+1
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * sci-libs/dealii: port to EAPI 6Matthias Maier2017-04-072-46/+46
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * sci-libs/dealii: version bump to 8.5.0Matthias Maier2017-04-072-0/+128
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * sci-mathematics/dolfin: Add dev-python/dijitso dependencyMatthias Maier2017-04-071-0/+1
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * dev-python/dijitso: initial commitMatthias Maier2017-04-073-0/+38
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * sci-mathematics/dolfin: fix runtime dependency on swigMatthias Maier2017-04-071-4/+5
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * sci-mathematics/dolfin: ebuild maintenanceMatthias Maier2017-04-072-7/+14
| | | | | | | | | | | | | | | | - add use flag descriptions to metadata - fix automagic dependencies - fix repoman warnings Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * sci-mathematics/dolfin: version bump to 2016.2.0Matthias Maier2017-04-063-0/+97
| | | | | | | | | | | | Further, bump to EAPI 6 and add dependencies Package-Manager: Portage-2.3.3, Repoman-2.3.2
| * fixup fiatMatthias Maier2017-04-061-1/+0
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