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* sci-biology/bwa: version bumpMartin Mokrejš2017-07-314-0/+75
| | | | | | | | | | | | | | | | | | | | | | | | Release 0.7.16 (30 July 2017) ----------------------------- This release added a couple of minor features and incorporated multiple pull requests, including: * Added option -5, which is useful to some Hi-C pipelines. * Fixed an error with samtools sorting (#129). Updated download link for GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple issues via a collected pull request #139 by @jmarshall. Avoid malformatted SAM header when -R is used with TAB (#84). Output mate CIGAR (#138). This release is expected to give the same alignment as 0.7.15, except the added mate-cigar tag. (0.7.16: 30 July 2017, r1180) https://lists.sourceforge.net/lists/listinfo/bio-bwa-help Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/ncbi-tools++: re-adding the patch with PCRE_LIBS addedMartin Mokrejš2017-07-281-4/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/ncbi-tools++: resolving my 'stash pop' with an empty changeMartin Mokrejš2017-07-281-1/+4
| | | | | | Sorry for noise. Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/libBigWig: remove old version with conflicting io.hMartin Mokrejš2017-07-282-26/+0
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/libBigWig: version bumpMartin Mokrejš2017-07-282-0/+26
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/nanopolish: new packageMartin Mokrejš2017-07-282-0/+60
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/vcftools: the 0.1.15_pre release was just renamed to 0.1.15 by ↵Martin Mokrejš2017-07-281-1/+1
| | | | | | upstream Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/ruffus: pint EGIT_REPO_URI to the archive URL of code.google.comMartin Mokrejš2017-07-281-2/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/picard: version bumpMartin Mokrejš2017-07-282-2/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/khmer: added a comment how to proceed with src_compile()Martin Mokrejš2017-07-281-1/+3
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/SPAdes: update comments on bundled dev-libs/boostMartin Mokrejš2017-07-281-1/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/MaSuRCA: add more URLs to HOMEPAGEMartin Mokrejš2017-07-281-2/+3
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/libBigWig: new release with io.h renamed to bigWigIO.hMartin Mokrejš2017-07-283-4/+4
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-biology/samtools: version bumpMartin Mokrejš2017-07-282-1/+1
| | | | | | | Cannot proceed unless htslib-1.5 can be properly installed along existing htslib-1.3.1 installation. Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/bcftools: version bumpMartin Mokrejš2017-07-282-0/+30
| | | | | | | This should be kept unmasked as it uses bundled static lib of htslib-1.5 so practically avoid dependency on sci-libs/htslib-1.5. Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-libs/htslib: version bumpMartin Mokrejš2017-07-282-0/+32
| | | | | | | Keeping KEYWORDS empty because it conflicts with htslib-1.3.1 as of now unless jlec/soap proceed in some proper way. Package-Manager: Portage-2.3.6, Repoman-2.3.2
* dev-lang/yaggo: version bump, fix install procedureMartin Mokrejš2017-07-282-4/+2
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/KING: new packageMartin Mokrejš2017-07-283-0/+48
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/trilinos: fix compilation with gcc-7Matthias Maier2017-07-142-1/+59
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* Update local USE descriptionJustin Lecher2017-07-091-2/+3
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/trilinos: bugfix - change eapply_user to epatch_user for EAPI 5Matthias Maier2017-07-071-1/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-libs/trilinos: add eapply_user to src_prepareMatthias Maier2017-07-071-0/+2
| | | | | | We'll have to migrate to EAPI 6 at some point Package-Manager: Portage-2.3.6, Repoman-2.3.2
* virtual/blas: eigen needs the fortran useflag to provide blas.François Bissey2017-07-073-3/+3
| | | | | Package-Manager: portage-2.3.6 Closes: https://github.com/gentoo/sci/pull/795
* sci-libs/libmaus: Bump to EAPI 6Justin Lecher2017-07-072-3/+3
| | | | | Package-Manager: Portage-2.3.6-prefix, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-visualization/mayavi: committed to gentoo main repo.Benda Xu2017-07-034-168/+0
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* sci-mathematics/slepc: fix SRC_URIMatthias Maier2017-06-301-1/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-libs/atlas: version bump to 3.11.39Gergely Nagy2017-06-273-0/+300
| | | | | | Patch from upstream is required to build the shared library: https://sourceforge.net/p/math-atlas/bugs/260/ Closes: https://github.com/gentoo/sci/pull/794
* sci-libs/atlas: Sanitize default USE combinationJustin Lecher2017-06-263-4/+4
| | | | | | | Helps sorting out #794 Package-Manager: Portage-2.3.6-prefix, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-geosciences/pydap_handlers_sql: Drop pacage due to dropped depsJustin Lecher2017-06-233-63/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-geosciences/pydap_handlers_cdms: Drop package due to masked depsJustin Lecher2017-06-233-48/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop www-client/casperjs due to broken revdepsJustin Lecher2017-06-237-54/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Add missing license for gamessJustin Lecher2017-06-231-0/+42
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/itk: bump to 4.12.0tharvik2017-06-232-0/+137
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1 Closes: https://github.com/gentoo/sci/pull/792
* sci-libs/dealii: ebuild maintenanceMatthias Maier2017-06-181-2/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-chemistry/acpype: Move from treeAlexey Shvetsov2017-06-163-0/+42
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-libs/acml: fix missed opencl depAndrew Savchenko2017-06-101-0/+98
| | | | | | | | | | | | 1) acml is linked with opencl support: libclFFT.so.2.3.1, libclBLAS.so.2.3.0, libacml_bridge.so.1.1.28: libOpenCL.so.1 => not found 2) update to EAPI 6. Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sci-libs/openblas: remove redundant libdir from Libs in .pcBenda Xu2017-06-061-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* numeric.eclass: use var reference in Libs and Cflags.Benda Xu2017-06-061-2/+2
| | | | Closes: https://github.com/gentoo/sci/issues/709
* sci-libs/cblas-reference: configure BLAS_LIBRARIES implicitlyBenda Xu2017-06-052-2/+0
| | | | | | | | | sci-libs/lapack-reference: configure BLAS_LIBRARIES implicitly cmake option USE_OPTIMIZED_BLAS uses pkg-config to figure out BLAS_LIBRARIES in Gentoo FindBLAS cmake patch. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/cblas-reference: guide cmake to find eselected blasBenda Xu2017-06-051-1/+1
| | | | | | | | | | same rational as commit e6181c66eac for lapack-reference. alternative.eclass blas.pc gives -L"${libdir}" -lxxx. The bare quotes confuses cmake parser. Escaping the quotes is tedious, but solves the problem. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/lapack-reference: guide cmake to find eselected blasBenda Xu2017-06-051-1/+1
| | | | | | | | alternative.eclass blas.pc gives -L"${libdir}" -lxxx. The bare quotes confuses cmake parser. Escaping the quotes is tedious, but solves the problem. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* Update local USE descriptionJustin Lecher2017-06-041-6/+6
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/pagmo: bump to pagmo2 and EAPI 6.Benda Xu2017-06-042-18/+18
| | | | | | Update the use flags. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/openblas: fix '??die' typos.Benda Xu2017-06-031-4/+4
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sys-cluster/openmpi: bump 2.0.3Justin Bronder2017-06-012-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sys-cluster/openmpi: bump 1.10.7Justin Bronder2017-06-012-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/gmsh: Drop oldMarius Brehler2017-05-292-90/+0
| | | | | | Required petsc versions were removed from the overlay. Package-Manager: Portage-2.3.5, Repoman-2.3.1
* Update README.mdMarius Brehler2017-05-291-3/+3
| | | | | | s/gentoo-sci/gentoo/g Signed-off-by: Marius Brehler <marbre@linux.sungazer.de>
* dev-python/nvidia-ml-py: Remove from overlayMarius Brehler2017-05-295-76/+0
| | | | | | | A matching version of nvidia-cuda-gdk is required, which is no longer available via the overlay. Signed-off-by: Marius Brehler <marbre@linux.sungazer.de>
* sci-libs/libsc: Removed, moved to ::gentooMatthias Maier2017-05-265-254/+0
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