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* app-admin/eselect: Version BumpJustin Lecher2018-04-024-6/+6
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/proovread: call perl_domodule to install *.pm filesMartin Mokrejs2018-04-021-0/+4
| | | | Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/proovread: new packageMartin Mokrejs2018-04-012-0/+62
| | | | | | Will need more work from upstream to make it into Gentoo. Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/diamond: new packageMartin Mokrejs2018-04-013-0/+40
| | | | | | | Do not know if the SSE instruction calls can be protected with CPU_FLAGS or similar. See page 2 in diamond_manual.pdf . Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genepop: switch to httpsMartin Mokrejs2018-04-011-2/+2
| | | | Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genepop: version bumpMartin Mokrejs2018-04-012-8/+8
| | | | | | | Upstream does not version the release tarballs, now 4.7 is being actually exposed on the website. Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/seq_crumbs: new packageMartin Mokrejs2018-04-013-0/+59
| | | | | | | The fix to setup.py to respect DESTDIR is probably not ideal. Needs a fix to avoid file collisions. Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/augustus: update file checksumMartin Mokrejs2018-03-311-1/+1
| | | | | | | | | | | | | | | | Seems upstream re-released the binary tarball with sources $ gzip -dc /usr/portage/distfiles/augustus-3.3.tar.gz | tar tvf - | grep 2018 drwxrwxr-x mario/mario 0 2018-01-26 14:09 augustus/auxprogs/homGeneMapping/src/ drwx------ mario/mario 0 2018-01-26 14:07 augustus/auxprogs/joingenes/ drwx------ mario/mario 0 2018-01-26 14:07 augustus/auxprogs/bam2hints/ drwx------ mario/mario 0 2018-01-26 14:09 augustus/auxprogs/filterBam/src/ drwxrwxr-x mario/mario 0 2018-01-26 14:09 augustus/auxprogs/filterBam/bin/ drwxrwxr-x mario/mario 0 2018-01-26 14:07 augustus/auxprogs/compileSpliceCands/ drwx------ mario/mario 0 2018-01-26 14:08 augustus/auxprogs/bam2wig/ drwx------ mario/mario 0 2018-01-26 14:08 augustus/bin/ Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/BRAKER: version bump, update LICENSEMartin Mokrejs2018-03-312-19/+13
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/bamql: new packageMartin Mokrejs2018-03-313-0/+41
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-mathematics/petsc: version bump to 3.8.4Matthias Maier2018-03-292-1/+1
| | | | Package-Manager: Portage-2.3.26, Repoman-2.3.7
* sci-biology/augustus: respect EPREFIX and new DEPENDencyMartin Mokrejs2018-03-231-3/+9
| | | | | | | The dependency is brought in through the comparative gene prediction code. Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/augustus: respect EPREFIX and enable comparative gene predictionMartin Mokrejs2018-03-231-0/+4
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/pysamstats: drop KEYWORDMartin Mokrejs2018-03-231-3/+3
| | | | | | needs working pysam, see bug #645060 Package-Manager: Portage-2.3.24, Repoman-2.3.6
* .travis.yml: Fix CIJustin Lecher2018-03-211-1/+2
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* .travis.yml: Update CIJustin Lecher2018-03-211-3/+3
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/dealii: update live ebuildMatthias Maier2018-03-192-4/+10
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-mathematics/petsc: fix dependencies, drop oldMatthias Maier2018-03-185-500/+6
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-mathematics/slepc: version bump to 3.8.2Matthias Maier2018-03-182-0/+75
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-mathematics/petsc: update 3.7.* to 3.7.7Matthias Maier2018-03-182-2/+2
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-mathematics/petsc: version bump to 3.8.3Matthias Maier2018-03-183-1/+223
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/amos: fix include path from -I$(top_builddir) to -I$(top_builddir)Martin Mokrejs2018-03-072-1/+26
| | | | | | | | | | | The include path is wrong when we use separate build directory. In file included from src/Bambus/Bundler/Utilities_Bundler.cc:4:0: src/Bambus/Bundler/Utilities_Bundler.hh:16:26: fatal error: Contig_AMOS.hh: No such file or directory https://sourceforge.net/p/amos/mailman/amos-help/thread/197db37d-d83e-1371-022b-2866c5686bd9%40fold.natur.cuni.cz/#msg36246774 Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-libs/trilinos: drop old versionsMatthias Maier2018-03-0110-2303/+0
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-libs/trilinos: version bump to 12.12.1Matthias Maier2018-03-014-1/+1311
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/ntCard: Add IUSE=openmp so one can disable OpenMPMartin Mokrejš2018-02-102-2/+14
| | | | Package-Manager: Portage-2.3.23, Repoman-2.3.6
* sci-biology/ntCard: new packageMartin Mokrejš2018-02-094-0/+59
| | | | Package-Manager: Portage-2.3.23, Repoman-2.3.6
* sci-biology/atsas: fix libsAlexey Shvetsov2018-02-091-1/+1
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/atsas: Add 2.8.3Alexey Shvetsov2018-02-092-0/+77
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/bam-readcount: use ${PV}Martin Mokrejš2018-02-031-2/+2
| | | | Package-Manager: Portage-2.3.23, Repoman-2.3.6
* sci-libs/tensorflow: Add second homepage urlMartin Mokrejš2018-01-292-2/+4
| | | | | Package-Manager: Portage-2.3.20, Repoman-2.3.6 RepoMan-Options: --force
* sci-biology/chiron: add the dependency on =sci-libs/tensorflow-1.0.1Martin Mokrejš2018-01-291-1/+1
| | | | | | | Seems tensorflow so changing a lot and versions are really incompatible with each other. Package-Manager: Portage-2.3.20, Repoman-2.3.6
* sci-biology/chiron: new packageMartin Mokrejš2018-01-292-0/+34
| | | | | | | Will need more work to get CPU- and GPU-based features enabled at once, or will need two separate installs? Package-Manager: Portage-2.3.20, Repoman-2.3.6
* sci-libs/tensorflow: new packageMartin Mokrejš2018-01-294-0/+68
| | | | | | | Will be needed for sci-biology/chiron, landing soon. Package-Manager: Portage-2.3.20, Repoman-2.3.6 RepoMan-Options: --force
* Unmask scilabJustin Lecher2018-01-271-4/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Convert linguas to l10nJustin Lecher2018-01-271-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-mathematics/scilab: Update to new localization handlingJustin Lecher2018-01-2712-59/+78
| | | | | | | Bump to EAPI=6 Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.20, Repoman-2.3.6
* Update Portage for travis to latestJustin Lecher2018-01-271-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop sparc-fbsd referenceJustin Lecher2018-01-272-10/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/mkl: Update to new localization handlingJustin Lecher2018-01-274-308/+4
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.20, Repoman-2.3.6
* dev-libs/intel-common: Update to new localization handlingJustin Lecher2018-01-271-5/+5
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.20, Repoman-2.3.6
* dev-lang/ifc: Update to new localization handlingJustin Lecher2018-01-271-6/+6
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.20, Repoman-2.3.6
* dev-lang/icc: Update to new localization handlingJustin Lecher2018-01-271-5/+5
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.20, Repoman-2.3.6
* sci-biology/rtg-tools: adjust descriptionMartin Mokrejš2018-01-261-1/+1
| | | | Package-Manager: Portage-2.3.20, Repoman-2.3.6
* sci-biology/rtg-tools: package skeletonMartin Mokrejš2018-01-262-0/+56
| | | | | | | | | | | Will need to ask upstream to provide common 'compile', 'install' and 'all' targets into https://github.com/RealTimeGenomics/rtg-tools/blob/master/build.xml Any volunteers to unbundle the bundled stuff? At least it is not gradle but good old ant. ;) Package-Manager: Portage-2.3.20, Repoman-2.3.6
* sci-biology/sga: add missing RDEPEND, more commentsMartin Mokrejš2018-01-251-1/+9
| | | | Package-Manager: Portage-2.3.19, Repoman-2.3.6
* sci-libs/fast5: document what is still broken in the ebuildMartin Mokrejš2018-01-241-0/+2
| | | | Package-Manager: Portage-2.3.19, Repoman-2.3.6
* sci-libs/fast5: version bump, fix compile paths for hdf5Martin Mokrejš2018-01-243-8/+8
| | | | Package-Manager: Portage-2.3.19, Repoman-2.3.6
* sci-biology/nanopolish: update compile procedure and depsMartin Mokrejš2018-01-241-3/+3
| | | | Package-Manager: Portage-2.3.19, Repoman-2.3.6
* sci-biology/pilon-bin: Drop the scala dependency for binary buildMartin Mokrejš2018-01-211-2/+1
| | | | Package-Manager: Portage-2.3.19, Repoman-2.3.6
* sci-biology/pilon-bin: Fix java runtime versionMartin Mokrejš2018-01-211-2/+2
| | | | Package-Manager: Portage-2.3.19, Repoman-2.3.6