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* enable new hashesJustin Lecher2017-12-021-5/+10
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/kraken: version bumpMartin Mokrejš2017-11-242-8/+6
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: execute jellyfish1 instead of jellyfishMartin Mokrejš2017-11-214-2/+130
| | | | | | | Also I wrote a few cleanup patches to expose THREADS variable and cleanup the code. Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/jellyfish: rename jellyfish to jellyfish1Martin Mokrejš2017-11-211-1/+3
| | | | | | | | | | This will facilitate simultaneous installs of jeelyfish2 and jellyfish, so that sci-biology/SEECER and sci-biology/quorum could be installed at the same time (both calling "jellyfish" but quorum needs version 2 and SEECER version 1. See list of files at https://packages.debian.org/unstable/jellyfish1 Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/BBmap: version bumpMartin Mokrejš2017-11-212-1/+1
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: 'patch -p1' and not 'patch -p0' is usedMartin Mokrejš2017-11-211-4/+4
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: drop trailing .ori from filenamesMartin Mokrejš2017-11-211-2/+2
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: remove stale .swp files from mschulzMartin Mokrejš2017-11-211-0/+1
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: adjust paths to work with patch -p1Martin Mokrejš2017-11-211-4/+4
| | | | | | | With bump to EAPI=6 the patch does not apply anymore due to extraneous 'SEECER-0.1.3/SEECER/'. Package-Manager: Portage-2.3.14, Repoman-2.3.6
* Second try to clean spaces in metadata.xmlJustin Lecher2017-11-18303-1590/+1590
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Consistently ident with tabsJustin Lecher2017-11-18830-6712/+6711
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bismark: Fix repoman warningsJustin Lecher2017-11-181-7/+8
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/trf-bin: Fix repoman warningsJustin Lecher2017-11-181-3/+4
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/trf: Fix repoman warningsJustin Lecher2017-11-181-5/+3
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/tmhmm: Fix repoman warningsJustin Lecher2017-11-182-4/+7
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/sequin: Fix repoman warningsJustin Lecher2017-11-181-4/+5
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/repeatmasker: Fix repoman warningsJustin Lecher2017-11-181-7/+6
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/fsl: Fix repoman warningsJustin Lecher2017-11-182-5/+5
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.14, Repoman-2.3.6
* dev-util/nvidia-cuda-gdk: Fix repoman warningsJustin Lecher2017-11-182-11/+7
| | | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.14, Repoman-2.3.6 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* dev-util/f90cache: Fix repoman warningsJustin Lecher2017-11-185-115/+2
| | | | | | | * Drop old Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.14, Repoman-2.3.6
* dev-lang/pgi: Bump to EAPI 6Justin Lecher2017-11-182-13/+11
| | | | | | | | * Fix repoman warnings Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.14, Repoman-2.3.6 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-visualization/mantid: Dropped due to missing dependencyJustin Lecher2017-11-184-156/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-physics/clip: Dropped due to missing dependencyJustin Lecher2017-11-183-52/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-chemistry/specView: Dropped due to missing dependencyJustin Lecher2017-11-187-370/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-chemistry/redcat: Drop due to unmet dependencyJustin Lecher2017-11-184-88/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-chemistry/chemBuild: Dropped due to unmet dependenciesJustin Lecher2017-11-186-188/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* dev-util/smartgit: Drop outdated version due to unmet dependencyJustin Lecher2017-11-183-62/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop keyqords due to unmet dependecyJustin Lecher2017-11-182-2/+2
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Bump portage version for travisJustin Lecher2017-11-181-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/HTSeq: In main treeDavid Seifert2017-11-163-39/+0
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* sci-biology/STAR: In main treeDavid Seifert2017-11-162-38/+0
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/lastz: fix long-lasting ebuild errors and version bumpMartin Mokrejš2017-11-163-8/+27
| | | | | | | | Seems Gentoo newer compiled/installed the lastz_32 binary, which allows indexing larger genomes. This ebuild fixes that for current version and contains practically same Makefile-related patch as before. Package-Manager: Portage-2.3.13, Repoman-2.3.3
* sci-biology/gbench: add missing SLOTMartin Mokrejš2017-11-161-1/+1
| | | | Package-Manager: Portage-2.3.13, Repoman-2.3.3
* sci-biology/gffutils: add missing DEPEND on dev-python/argcompleteMartin Mokrejš2017-11-161-1/+2
| | | | Package-Manager: Portage-2.3.13, Repoman-2.3.3
* sci-biology/gffutils: add missing DEPEND on dev-python/arghMartin Mokrejš2017-11-161-1/+2
| | | | Package-Manager: Portage-2.3.13, Repoman-2.3.3
* sci-biology/gffutils: add missing DEPEND on dev-python/simplejsonMartin Mokrejš2017-11-161-1/+3
| | | | Package-Manager: Portage-2.3.13, Repoman-2.3.3
* sci-biology/bamtools: Remove, everything in main treeDavid Seifert2017-11-024-93/+0
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* Update travis checks to latest portage versionJustin Lecher2017-10-301-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sys-cluster/htcondor: Remove optional dep on net-libs/qmfDavid Seifert2017-10-153-29/+21
| | | | Package-Manager: Portage-2.3.11, Repoman-2.3.3
* profiles: remove use.local.desc permanentlyDavid Seifert2017-10-152-402/+8
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* profiles: update use.local.desc for sci-libs/dealii flagsDavid Seifert2017-10-141-0/+3
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* sci-libs/dealii: update live ebuildMatthias Maier2017-10-072-3/+13
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-mathematics/petsc: fix build on knem setupsAndrew Savchenko2017-10-031-0/+2
| | | | | | | If host MPI is configured to use knem, petsc needs to access /dev/knem as well. Package-Manager: Portage-2.3.8, Repoman-2.3.3 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sci-mathematics/petsc: fix superlu version requirementAndrew Savchenko2017-10-031-1/+1
| | | | | | | | | >=sci-libs/superlu-5 is required, see https://lists.debian.org/debian-science/2016/05/msg00059.html This also happens at our local Gentoo HPC setup. Package-Manager: Portage-2.3.8, Repoman-2.3.3 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sci-libs/gsl: bump to gsl-2.4.François Bissey2017-09-235-4/+83
| | | | | | | | | Change over to https in all ebuilds to keep repoman happy. Closes: https://github.com/gentoo/sci/pull/815 Closes: https://github.com/gentoo/sci/issues/813 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sys-cluster/openmpi: bump 2.1.2Justin Bronder2017-09-222-4/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.1
* sci-visualization/mricrogl: version bump.Horea Christian2017-09-212-0/+42
| | | | | Closes: https://github.com/gentoo/sci/pull/798 Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/fsl: version bump.Horea Christian2017-09-216-1/+732
| | | | | | | made env.dfile prefix-compatible Closes: https://github.com/gentoo/sci/pull/804 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-mathematics/dolfin and reverse deps: fix PYTHON_COMPATMatthias Maier2017-09-146-6/+6
| | | | Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/dolfin: fix patch nameMatthias Maier2017-09-141-1/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3