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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
* sci-biology/barrnap: respect EPREFIXMartin Mokrejš2017-04-252-4/+4
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* 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, 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
* 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-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-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
* sci-biology/nxtrim: drop patch accepted by upstream nowMartin Mokrejš2017-04-122-48/+0
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/ncbi-tools++: add note on idfetch collision by upstreamMartin Mokrejš2017-04-111-0/+6
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/freebayes: use https instead of git protocolMartin Mokrejš2017-04-071-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-biology/nxtrim: use proper protocol nameMartin Mokrejš2017-04-071-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-biology/nxtrim: just opened an issue #32 with upstreamMartin Mokrejš2017-04-071-1/+1
| | | | | | https://github.com/sequencing/NxTrim/issues/32 Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-biology/igv: fix SLOTs in ebuildMartin Mokrejš2017-04-074-14/+14
| | | | | | | Notably because Gentoo has no more guava-17 we depend on never, untested version guava-20. Upstream does not guarantee IGV will work with newer dependencies properly. Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-biology/nxtrim: new packageMartin Mokrejš2017-04-063-0/+83
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-biology/igv: fix SLOT operatorsMartin Mokrejš2017-04-032-15/+15
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-biology/BBmap: add ~x86 to KEYWORDS, version bumpMartin Mokrejš2017-04-036-4/+47
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-biology/igv: version bump, cannot compile ↵Martin Mokrejš2017-04-032-0/+88
| | | | | | | | | | | | | | | | | | | | | | | | FlowSignalDistributionPanel.java:222 It seem this is related to Gentoo ebuild unbundling some of the bundled libs. I can compile vanilla sources using ant without this issue. [javac] Compiling 889 source files to /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/tmp [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:33: warning: NotImplementedException is internal proprietary API and may be removed in a future release [javac] import sun.reflect.generics.reflectiveObjects.NotImplementedException; [javac] ^ [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable [javac] dataset.addValue(data[j], seriename, cat); [javac] ^ [javac] class file for org.jfree.util.PublicCloneable not found [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:266: error: cannot access Drawable [javac] CategoryPlot plot = freechart.getCategoryPlot(); [javac] ^ [javac] class file for org.jfree.ui.Drawable not found [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:102: warning: NotImplementedException is internal proprietary API and may be removed in a future release [javac] throw new NotImplementedException(); Package-Manager: Portage-2.3.5, Repoman-2.3.1
* Merge remote-tracking branch 'github/master'Marius Brehler2017-04-032-2/+30
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| * sci-biology/nilearn: importing system joblib (#762)Horea Christian2017-03-272-2/+30
| | | | | | | | | | | | | | | | | | | | * sci-biology/nilearn: importing system joblib Package-Manager: Portage-2.3.4, Repoman-2.3.2 * sci-biology/nilearn: declaring local variable Package-Manager: Portage-2.3.4, Repoman-2.3.2
* | sci-biology/libBigWig: manually pass DESTDIR variableMartin Mokrejš2017-03-312-0/+8
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/libBigWig: respect DESTDIRMartin Mokrejš2017-03-312-2/+12
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/plinkseq: we cannot zap bundled mongoose so easilyMartin Mokrejš2017-03-311-5/+8
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/deeptools: add new packageMartin Mokrejš2017-03-314-0/+77
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | Revert "sci-biology/deeptools: add a new package"Martin Mokrejš2017-03-317-182/+6
| | | | | | | | This reverts commit 81a1355ea065924e0c6426772af7c16d90432ccd.
* | sci-biology/deeptools: add a new packageMartin Mokrejš2017-03-317-6/+182
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/libBigWig: ebuild cleanup, add last released versionMartin Mokrejš2017-03-314-0/+47
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/ncbi-tools++: avoid file collision, KEYWORDS added backMartin Mokrejš2017-03-271-2/+2
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/ncbi-tools++: compiles via 'make -j1' nowMartin Mokrejš2017-03-272-0/+29
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/ncbi-tools++: and moreMartin Mokrejš2017-03-273-0/+32
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/ncbi-tools++: fix table2asn linkingMartin Mokrejš2017-03-272-0/+14
| | | | | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1
* | sci-biology/ncbi-tools++: more fixesMartin Mokrejš2017-03-264-2/+28
|/ | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/hisat2: Properly support pythonJustin Lecher2017-03-261-5/+8
| | | | | | | Drop stray CVS header line Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/scbi_zcat: Drop obsolete ruby versionJustin Lecher2017-03-261-4/+6
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/scbi_plot: Drop obsolete ruby versionJustin Lecher2017-03-261-4/+6
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/scbi_mapreduce: Drop obsolete ruby versionJustin Lecher2017-03-261-4/+6
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/scbi_fastq: Drop obsolete ruby versionJustin Lecher2017-03-261-4/+6
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/scbi_fasta: Drop obsolete ruby versionJustin Lecher2017-03-261-3/+4
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/scbi_blast: Drop obsolete ruby versionJustin Lecher2017-03-261-4/+6
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/full_lengther_next: Drop obsolete ruby versionJustin Lecher2017-03-261-4/+6
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bio-cd-hit-report: Drop obsolete ruby versionJustin Lecher2017-03-261-4/+6
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Remove broken packageJustin Lecher2017-03-263-47/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/MolBioLib: Add missing SLOT operatorJustin Lecher2017-03-261-3/+4
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop masked package - sci-biology/artemis-binJustin Lecher2017-03-263-80/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop masked package - sci-biology/gbrowseJustin Lecher2017-03-2615-983/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>