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2018-10-21gnu: flexbar: Update to 3.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0. [source]: Fetch from git. [arguments]: Adjust check and install phases. [home-page]: Update to new home at Github. [license]: Change to bsd-3.
2018-10-21gnu: seqan: Update to 2.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0. [native-inputs]: Replace bzip2 with xz. (seqan-1): New variable. (tophat)[inputs]: Use seqan-1.
2018-10-21gnu: khmer: Update to 2.1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2. [source]: Fetch from git; remove bundled libraries in snippet. [arguments]: Remove "set-paths" phase; remove "post-install-check" phase; remove "reset-gzip-timestamps" phase. [native-inputs]: Remove seqan and python-nose; add python-cython, python-pytest, and python-pytest-runner. [inputs]: Remove gcc-4.9.
2018-10-21gnu: python-screed: Update to 1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.0. [arguments]: Run tests after installation. [native-inputs]: Add python-pytest, python-pytest-cov, and python-pytest-runner; remove python-nose.
2018-10-21gnu: fasttree: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify install phase.
2018-10-21gnu: express-beta-diversity: Update to 1.0.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8. [source]: Fetch from git. [arguments]: Use INVOKE; remove "exit-source" build phase; simplify.
2018-10-21gnu: edirect: Update to 10.2.20181018.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018. [arguments]: Add simple check phase; simplify other phases. [inputs]: Add perl-xml-simple.
2018-10-21gnu: eigensoft: Update to 7.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1. [arguments]: Remove Makefile modification.
2018-10-21gnu: discrover: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
2018-10-21gnu: diamond: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
2018-10-21gnu: delly: Update to 0.7.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9. [source]: Fetch from git. [arguments]: Add phase install-templates; use default install phase. [native-inputs]: Remove python-2. [home-page]: Use new home page. * gnu/packages/patches/delly-use-system-libraries.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21gnu: deeptools: Update to 3.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
2018-10-21gnu: python-dendropy: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
2018-10-21gnu: python-py2bit: Update to 0.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
2018-10-21gnu: cutadapt: Update to 1.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio.
2018-10-21gnu: Add python-dnaio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
2018-10-21gnu: crossmap: Update to 0.2.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9. * gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21gnu: python-twobitreader: Update to 3.1.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git.
2018-10-21gnu: Add python-bx-python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python.
2018-10-21gnu: python2-bx-python: Update to 0.8.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2. [source]: Remove obsolete snippet. [inputs]: Move python2-numpy from here... [propagated-inputs]: ...to here; add python2-six. [native-inputs]: Add python2-lzo and python2-cython. [home-page]: Update to new home at Github.
2018-10-21gnu: bwa-pssm: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
2018-10-21gnu: tophat: Update to 2.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1. * gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21gnu: python2-dendropy: Disable failing test.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable failing test.
2018-10-20gnu: bowtie: Update to 2.3.4.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3. [source]: Fetch from git. [inputs]: Replace python-2 with python-wrapper; move perl, perl-clone, perl-test-deep, and perl-test-simple from here... [native-inputs]: ...to here. [arguments]: Simplify check phase.
2018-10-20gnu: blast+: Use INVOKE and return #T unconditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and return #T unconditionally.
2018-10-20gnu: bedops: Update to 2.4.35.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35. [source]: Fetch from git.
2018-10-20gnu: bedops: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
2018-10-20gnu: bamm: Fetch from git and use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git. [arguments]: Use INVOKE and return #T unconditionally.
2018-10-20gnu: aragorn: Use invoke and simplify.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build phase; simplify install phase.
2018-10-20gnu: clipper: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1. [source]: Fetch from git. [arguments]: Add fix-typo phase.
2018-10-20gnu: python-pybedtools: Update to 0.7.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10. [arguments]: Disable broken tests. [propagated-inputs]: Replace bedtools with bedtools-2.26; add python-matplotlib, python-pysam, and python-pyyaml. [native-inputs]: Remove python-pyyaml; add kentutils, python-numpy, python-pandas, and python-six. (python-pybedtools): New variable.
2018-10-20gnu: Add bedtools-2.26.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
2018-10-11gnu: kallisto: Update to 0.44.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.44.0. [source]: Fetch from git. [arguments]: Add build phase to use htslib from Guix. [inputs]: Add htslib.
2018-10-08gnu: Add filtlong.pimi
* gnu/packages/bioinformatics.scm (filtlong): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-10-05gnu: Add ngless.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless): New variable.
2018-10-05gnu: bioruby: Update to 1.5.2.Christopher Baines
This works with Ruby 2.5. * gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
2018-10-05gnu: samtools-0.1: Adjust to match changes in samtools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make flags.
2018-10-05gnu: deeptools: Update to 3.1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2. [source]: Fetch from git. [arguments]: Delete reset-gzip-timestamps phase. [inputs]: Add python-plotly.
2018-10-05gnu: python-pysam: Update to 0.15.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.15.1. [source]: Fetch from git. [arguments]: Delete tests requiring internet access; use "invoke". [inputs]: Add curl.
2018-10-05gnu: bcftools: Update to 1.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9. [arguments]: Remove obsolete make flags.
2018-10-05gnu: samtools: Update to 1.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools): Update to 1.9. [origin]: Remove bundled htslib sources. [arguments]: Remove obsolete make-flags.
2018-10-05gnu: htslib: Update to 1.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
2018-10-02gnu: Add r-absfiltergsea.pimi
* gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.
2018-10-02gnu: Add poretools.pimi
* gnu/packages/bioinformatics.scm (poretools): New variable.
2018-09-30gnu: Add porechop.pimi
* gnu/packages/bioinformatics.scm (porechop): New variable.
2018-09-24gnu: Add r-bseqsc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
2018-09-24gnu: Add r-cssam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cssam): New variable.
2018-09-24gnu: Add r-xbioc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
2018-09-22gnu: hmmer: Update to 3.2.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1. [origin]: Remove patch. [license]: Change to BSD-3. [supported-systems]: New field. * gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2018-09-21gnu: Add r-pore.pimi
* gnu/packages/bioinformatics.scm (r-pore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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