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* sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl ↵Martin Mokrejš2014-04-029-1/+14
| | | | | | scripts to fix situations when user has for some reason an empty CONSED_HOME Package-Manager: portage-2.2.7
* sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is ↵Martin Mokrejš2014-03-312-18/+22
| | | | | | available system-wide, upstream https://github.com/ged-lab/khmer/pull/346 Package-Manager: portage-2.2.7
* sci-biology/YASRA: version bump to a version without compile errors when ↵Martin Mokrejš2014-03-313-3/+9
| | | | | | gcc-4.8 is used Package-Manager: portage-2.2.7
* sci-biology/RADtools: new packageMartin Mokrejš2014-03-315-0/+95
| | | | Package-Manager: portage-2.2.7
* sci-biology/tablet: skeleton for a new package eventually to replace current ↵Martin Mokrejš2014-03-316-0/+224
| | | | | | tablet-bin package Package-Manager: portage-2.2.7
* sci-biology/stacks: skeleton for a new package; needs webapp team help, ↵Martin Mokrejš2014-03-314-0/+69
| | | | | | *some* Makefile's need proper DESTDIR support Package-Manager: portage-2.2.7
* sci-biology/biopieces: skeleton for a new package; has it's own install.sh ↵Martin Mokrejš2014-03-315-0/+147
| | | | | | script Package-Manager: portage-2.2.7
* sci-biology/scan_for_matches: new package, LICENSE not explicitly avalaible ↵Martin Mokrejš2014-03-314-0/+46
| | | | | | hence seems public-domain fits? Package-Manager: portage-2.2.7
* sci-biology/ncbi-tools++: add deps on jpeg-turboMartin Mokrejš2014-03-251-1/+1
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* sci-biology/cutadapt: switch to use newer source code location, add support ↵Martin Mokrejš2014-03-254-2/+60
| | | | for github snapshots, version bump
* sci-biology/khmer: Also drop sphinx as build requirementJustin Lecher2014-03-243-0/+6
| | | | Package-Manager: portage-2.2.9-r1
* sci-biology/staden: fix ESVN_REPO_URI to include trailing 'src/' so that we ↵Martin Mokrejš2014-03-242-4/+5
| | | | | | do not have to change ''. Thanks to Justin Lercher for the patch. Package-Manager: portage-2.2.7
* sci-biology/ngs_backbone: added an ebuild for latest releaseMartin Mokrejš2014-03-245-0/+179
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* sci-biology/mgblast: initial ebuild but while it needs an old version of ↵Martin Mokrejš2014-03-244-0/+67
| | | | ncbi-tools source tree to build ... it is not tested yet
* sci-biology/BamView: dropped KEYWORDSMartin Mokrejš2014-03-242-1/+5
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* sci-biology/BamView: not sure if we need a separate package; is said to be ↵Martin Mokrejš2014-03-243-0/+31
| | | | part of Artemis bundle
* sci-biology/mapview-bin: new package, missing LICENSE, upstream website is downMartin Mokrejš2014-03-244-0/+51
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* sci-biology/emboss-6.3.1_p4-r2: added plplot dependency, trying to get rid ↵Martin Mokrejš2014-03-242-4/+14
| | | | | | of a Makefile.patch using sed hackery Package-Manager: portage-2.2.7
* sci-biology/freebayes: a new package skeleton; need to retrive from git in a ↵Martin Mokrejš2014-03-243-0/+49
| | | | recursive way
* sci-biology/pileup: dropped KEYWORDS due to misisng LICENSEMartin Mokrejš2014-03-242-2/+6
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* sci-biology/pileup: new package; a pileup pipeline used along SSAHA2Martin Mokrejš2014-03-244-0/+86
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* sci-biology/sga: new package; forces its own optimization flags but works fineMartin Mokrejš2014-03-243-0/+66
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* sci-biology/ngsview: new package skeleton, needs qt team helpMartin Mokrejš2014-03-244-0/+47
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* sci-biology/scythe: new package, bundled Makefile forces -O3, wrong version ↵Martin Mokrejš2014-03-243-0/+45
| | | | number, but works
* sci-biology/sickle: new packageMartin Mokrejš2014-03-243-0/+45
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* API bumped, whitespace removalMartin Mokrejš2014-03-242-2/+5
| | | | Package-Manager: portage-2.2.7
* added some dev-java dependencies and removed some bundled .jar filesMartin Mokrejš2014-03-242-1/+68
| | | | Package-Manager: portage-2.2.7
* sci-biology/artemis-bin: documented dependencesMartin Mokrejš2014-03-242-1/+5
| | | | Package-Manager: portage-2.2.7
* sci-biology/artemis: documented dependencesMartin Mokrejš2014-03-242-0/+5
| | | | Package-Manager: portage-2.2.7
* sci-biology/igv-2.0.35: version bumpMartin Mokrejš2014-03-232-2/+41
| | | | Package-Manager: portage-2.2.7
* sci-biology/consed2gap: new package, worksMartin Mokrejš2014-03-234-0/+57
| | | | Package-Manager: portage-2.2.7
* sci-biology/inGAP-bin: new package; needs java team helpMartin Mokrejš2014-03-234-0/+58
| | | | Package-Manager: portage-2.2.7
* sci-biology/eval: new package; needs perl team help to install this evil ↵Martin Mokrejš2014-03-234-0/+54
| | | | package with Eval.pm into PERL_PATH
* sci-biology/cgview-bin: new package, needs java team helpMartin Mokrejš2014-03-234-0/+41
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* sci-biology/cgview-bin: new package, needs java team testing, maybe ↵Martin Mokrejš2014-03-234-0/+64
| | | | | | dev-java/batik is misisng svg USE flag? Package-Manager: portage-2.2.7
* sci-biology/CONTIGuator: a skeleton for a new package, needs ↵Martin Mokrejš2014-03-233-0/+27
| | | | sci-biology/artemis or sci-biology/artemis-bin
* sci-biology/Atlas2: a skeleton for a new package, needs help from ruby teamMartin Mokrejš2014-03-234-0/+61
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* sci-biology/MAKER: a skeleton for a new packageMartin Mokrejš2014-03-233-0/+41
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* sci-biology/IMAGE: a skeleton for a new packageMartin Mokrejš2014-03-234-0/+39
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* sci-biology/ruffus: new package, maybe better to place it under dev-python/Martin Mokrejš2014-03-233-0/+43
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* sci-biology/MaSuRCA: new package but with a missing LICENSE and needs tweak ↵Martin Mokrejš2014-03-231-0/+8
| | | | to get all configure's running
* sci-biology/MaSuRCA: new package but with a missing LICENSE and needs tweak ↵Martin Mokrejš2014-03-233-0/+74
| | | | to get all configure's running
* sci-biology/scaffold_builder: new package but with a missing LICENSEMartin Mokrejš2014-03-234-0/+53
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* sci-biology/SolexaQA: new packageMartin Mokrejš2014-03-234-0/+43
| | | | Package-Manager: portage-2.2.7
* sci-biology/skewer-bin: new packageMartin Mokrejš2014-03-234-0/+45
| | | | Package-Manager: portage-2.2.7
* sci-biology/BBmap: a skeleton for a new package, needs help from java team ↵Martin Mokrejš2014-03-234-0/+46
| | | | for sure
* sci-biology/jtreeview: a skeleton for a new package, needs help from java ↵Martin Mokrejš2014-03-231-0/+9
| | | | team for sure
* sci-biology/jtreeview: a skeleton for a new package, needs help from java ↵Martin Mokrejš2014-03-232-0/+26
| | | | team for sure
* sci-biology/fsa: new package, enforces its own CXXFLAGS, compiles also some ↵Martin Mokrejš2014-03-234-0/+39
| | | | | | java stuff, source code does not compile Package-Manager: portage-2.2.7
* sci-biology/artemis: fixed JVM dependency, added a link to INSTALL docsMartin Mokrejš2014-03-232-3/+7
| | | | Package-Manager: portage-2.2.7