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* sci-biology/imagej: Do not call external programs in global scopeDavid Seifert2017-09-071-1/+1
| | | | | Closes: https://bugs.gentoo.org/show_bug.cgi?id=630214 Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-libs/htslib: Remove oldDavid Seifert2017-09-025-103/+0
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* sci-biology/samtools: Remove oldDavid Seifert2017-09-0214-1041/+0
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* sci-biology/bcftools: Remove oldDavid Seifert2017-09-025-105/+0
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* sci-biology/pysam: Remove oldDavid Seifert2017-09-024-66/+0
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* sci-biology/scbi_zcat: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/scbi_plot: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/scbi_mapreduce: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/scbi_fastq: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/scbi_fasta: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/scbi_blast: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/full_lengther_next: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/biopieces: Update USE_RUBY to fix breakagesDavid Seifert2017-09-022-4/+4
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/bio-cd-hit-report: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-biology/Atlas2: Update USE_RUBY to fix breakagesDavid Seifert2017-09-021-1/+1
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* profiles: Remove last mentions of sci-libs/acmlDavid Seifert2017-09-025-470/+1
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* dev-lang/pgi: Remove last mentions of sci-libs/acmlDavid Seifert2017-09-022-11/+3
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-libs/clblas: Remove last mentions of sci-libs/acmlDavid Seifert2017-09-023-3/+0
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* virtual/blas: Remove last mentions of sci-libs/acmlDavid Seifert2017-09-023-3/+0
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* sci-libs/acml: Already removed from main treeDavid Seifert2017-09-025-344/+0
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* sci-biology/bwa: Latest in main treeDavid Seifert2017-09-024-75/+0
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* numeric-int64-multibuild.eclass: consider _static build variant.Benda Xu2017-08-291-5/+11
| | | | | | | | _static is considered to be a different variant in this eclass, but is no different from its dynamic conterpart in multilib.eclass. Credit: Tom Daff Closes: https://github.com/gentoo/sci/issues/809
* sci-libs/openblas: USE flags of single-threaded version.Benda Xu2017-08-281-0/+2
| | | | | | | | When neither openmp nor threads USE flag is set, OpenBLAS should build a single-threaded version with make option USE_THREAD=0. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sys-cluster/modules: remove oldAndrew Savchenko2017-08-254-149/+0
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sys-cluster/modules: make repoman happy about dosymAndrew Savchenko2017-08-251-1/+1
| | | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sys-cluster/modules: bump to EAPI 6Andrew Savchenko2017-08-253-1/+87
| | | | | | | | | | For modules-3.2.10-r2: - bump to EAPI 6 - fix sh.in template - fix gcc warnings Package-Manager: Portage-2.3.8, Repoman-2.3.3 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sci-libs/openblas: fix DESTDIR and PREFIX for cmake directories.Benda Xu2017-08-254-12/+12
| | | | | | Closes: https://github.com/gentoo/sci/pull/725 Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/openblas: Bump to 0.2.20.François Bissey2017-08-258-73/+345
| | | | | | | | | | Clean up after fixing multilib wrapper issue. Use https to make repoman happy. Closes: https://github.com/gentoo/sci/pull/800 Bug: 617312 Package-Manager: Portage-2.3.6, Repoman-2.3.3
* numeric-int64-multibuild.eclass: MULTILIB_ABI_FLAG should be USE flagBenda Xu2017-08-251-5/+16
| | | | | | | The multilib-build eclass expects MULTILIB_ABI_FLAG to be USE flags. If it is set to be ABI, the headers will not be included. Bug: 617312
* sci-libs/nipype: added dependenciesHorea Christian2017-08-251-0/+3
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-libs/nipy: version bumpHorea Christian2017-08-253-14/+55
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* sci-libs/nibabel: fixed indentationHorea Christian2017-08-252-17/+17
| | | | Package-Manager: Portage-2.3.8, Repoman-2.3.3
* Add necessary variable to allow multilib wrapping of headersFrançois Bissey2017-08-231-0/+1
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* sci-libs/dealii: update live ebuild to upstream changesMatthias Maier2017-08-142-3/+9
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.3
* 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