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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-biology/KING: new packageMartin Mokrejš2017-07-283-0/+48
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/verifyBamID: another attempt at removing the -WerrorMartin Mokrejš2017-05-251-4/+3
| | | | | | | Somehow the sed calls do not work, disable -Werror append by defining the variable non-empty Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/verifyBamID: work around compile error with g++-7.1.0Martin Mokrejš2017-05-251-0/+3
| | | | | | https://github.com/statgen/verifyBamID/issues/7 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/ncbi-tools++: do not add $(PCRE_LIBS) unless necessary (from ↵Martin Mokrejš2017-05-238-198/+97
| | | | | | Aaron Ucko) Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/cortex_var: fix compilation error on PREFIXed hostsMartin Mokrejš2017-05-221-1/+2
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SOAPdenovo2: add Debian manpageMartin Mokrejš2017-05-223-5/+25
| | | | | | https://manpages.debian.org/testing/soapdenovo2/soapdenovo2.1.en.html Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/samtools: Add missing SLOT operatorsJustin Lecher2017-05-226-9/+9
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/cortex_var: EAPI bump and QA FixesJustin Lecher2017-05-222-11/+15
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/angsd: QA FixesJustin Lecher2017-05-221-1/+1
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/vcftools: QA FixesJustin Lecher2017-05-222-4/+5
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/cutadapt: add recent new dependencyMartin Mokrejš2017-05-212-2/+6
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/MaSuRCA: version bumpMartin Mokrejš2017-05-163-58/+35
| | | | | | | The package is actually a bundle of many, including SOAPdenovo2 somewhat patched so that it compiles (unlike vanilla 2.04-r240). Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SOAPdenovo2: a bit cleanup of the build processMartin Mokrejš2017-05-161-2/+28
| | | | | | Will need to bring in Debian med patches from git://anonscm.debian.org/debian-med/soapdenovo2.git Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SOAPdenovo2: new packageMartin Mokrejš2017-05-153-0/+33
| | | | | | Does not respect CFLAGS, compile fails Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/quorum: improve DESCRIPTION textMartin Mokrejš2017-05-152-3/+3
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/jellyfish: point SRC_URI to proper tarball, drop yaggo DEPENDencyMartin Mokrejš2017-05-152-5/+3
| | | | | | | This tarball really doe snot need yaggo for building. See for whole discussion: https://github.com/gmarcais/Jellyfish/issues/87 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/jellyfish: CDEPEND does not work?Martin Mokrejš2017-05-151-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/jellyfish: version bump, add new CDEPEND on dev-lang/yaggoMartin Mokrejš2017-05-152-6/+14
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/quorum: version bumpMartin Mokrejš2017-05-152-4/+6
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: drop DEPENDency on boostMartin Mokrejš2017-05-141-6/+8
| | | | | | | Upstream says SPAdes uses bundled while modified local copy. Fix URL to new official site. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: install the package directly using cmakeMartin Mokrejš2017-05-141-3/+5
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: fix compile issue but drop KEYWORDS because of QA issuesMartin Mokrejš2017-05-133-10/+49
| | | | | | | | | | Use patch from https://github.com/Homebrew/homebrew-science/pull/5616 The package install its own *.py files outside of PYTHON's site-packages/. The "make install" procedure is flakey shellscript and there is no setup.py so we could reuse common infrastructure for pythonic packages. There are plenty of bundled 3rd-party apps, some of them compiling statically. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: improve DESCRIPTIONMartin Mokrejš2017-05-131-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/poretools: new packageMartin Mokrejš2017-05-133-0/+39
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: version bumpMartin Mokrejš2017-05-122-5/+5
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/BBmap: version bumpMartin Mokrejš2017-05-112-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/last: version bumpMartin Mokrejš2017-05-105-0/+161
| | | | | | | The src_install() part does not re-introduce the *.sh and *.py file extensions like previous -299 ebuild. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/angsd: add default() to make EAPI=6 happyMartin Mokrejš2017-05-011-1/+2
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/stacks: rely on SLOT 0 of htslib < 1.4Martin Mokrejš2017-04-301-1/+1
| | | | | | Supposedly stacks would not work with htslib-1.4 which provides libhtslib.so.2 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/stacks:Martin Mokrejš2017-04-301-4/+5
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/oncotator: note that python-3.x is not supportedMartin Mokrejš2017-04-301-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/bcftools: version bumpMartin Mokrejš2017-04-302-0/+30
| | | | | | Compiles its own static build of htslib-1.4 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/samtools: version bumpMartin Mokrejš2017-04-302-0/+83
| | | | | | | Compiles fine against htslib-1.4 but because htslib-1.4 is not KEYWORDed keeping samtools-1.4 masked as well. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* Cleanup remote IDsJustin Lecher2017-04-30104-141/+122
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Add new remote IDJustin Lecher2017-04-291-1/+4
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>