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* gnu: r-gprofiler: Update to 0.6.7.•••* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.7. Ricardo Wurmus2018-10-30
* gnu: r-keggrest: Update to 1.20.2.•••* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.2. Ricardo Wurmus2018-10-30
* gnu: r-msnbase: Update to 2.6.4.•••* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.4. Ricardo Wurmus2018-10-30
* gnu: r-methylkit: Update to 1.6.3.•••* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.3. Ricardo Wurmus2018-10-30
* gnu: r-wgcna: Update to 1.66.•••* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.66. Ricardo Wurmus2018-10-30
* gnu: r-go-db: Update to 3.6.0.•••* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.6.0. Ricardo Wurmus2018-10-30
* gnu: r-genomicfeatures: Update to 1.32.3.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.3. Ricardo Wurmus2018-10-30
* gnu: r-delayedarray: Update to 0.6.6.•••* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.6. Ricardo Wurmus2018-10-30
* gnu: r-genomicranges: Update to 1.32.7.•••* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.7. Ricardo Wurmus2018-10-30
* gnu: r-limma: Update to 3.36.5.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.5. Ricardo Wurmus2018-10-30
* gnu: r-edger: Update to 3.22.5.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.5. Ricardo Wurmus2018-10-30
* gnu: r-genomeinfodbdata: Update to 1.1.0.•••* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.1.0. Ricardo Wurmus2018-10-30
* gnu: r-iranges: Update to 2.14.12.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.12. Ricardo Wurmus2018-10-30
* gnu: r-vegan: Update to 2.5-3.•••* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-3. Ricardo Wurmus2018-10-30
* gnu: flexbar: Update to 3.4.0.•••* 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. Ricardo Wurmus2018-10-21
* gnu: seqan: Update to 2.4.0.•••* 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. Ricardo Wurmus2018-10-21
* gnu: khmer: Update to 2.1.2.•••* 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. Ricardo Wurmus2018-10-21
* gnu: python-screed: Update to 1.0.•••* 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. Ricardo Wurmus2018-10-21
* gnu: fasttree: Use INVOKE.•••* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify install phase. Ricardo Wurmus2018-10-21
* gnu: express-beta-diversity: Update to 1.0.8.•••* 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. Ricardo Wurmus2018-10-21
* gnu: edirect: Update to 10.2.20181018.•••* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018. [arguments]: Add simple check phase; simplify other phases. [inputs]: Add perl-xml-simple. Ricardo Wurmus2018-10-21
* gnu: eigensoft: Update to 7.2.1.•••* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1. [arguments]: Remove Makefile modification. Ricardo Wurmus2018-10-21
* gnu: discrover: Fetch from git.•••* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git. Ricardo Wurmus2018-10-21
* gnu: diamond: Fetch from git.•••* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git. Ricardo Wurmus2018-10-21
* gnu: delly: Update to 0.7.9.•••* 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. Ricardo Wurmus2018-10-21
* gnu: deeptools: Update to 3.1.3.•••* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3. Ricardo Wurmus2018-10-21
* gnu: python-dendropy: Fetch from git.•••* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git. Ricardo Wurmus2018-10-21
* gnu: python-py2bit: Update to 0.3.0.•••* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0. Ricardo Wurmus2018-10-21
* gnu: cutadapt: Update to 1.18.•••* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio. Ricardo Wurmus2018-10-21
* gnu: Add python-dnaio.•••* gnu/packages/bioinformatics.scm (python-dnaio): New variable. Ricardo Wurmus2018-10-21
* gnu: crossmap: Update to 0.2.9.•••* 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. Ricardo Wurmus2018-10-21
* gnu: python-twobitreader: Update to 3.1.6.•••* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git. Ricardo Wurmus2018-10-21
* gnu: Add python-bx-python.•••* gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python. Ricardo Wurmus2018-10-21
* gnu: python2-bx-python: Update to 0.8.2.•••* 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. Ricardo Wurmus2018-10-21
* gnu: bwa-pssm: Fetch from git.•••* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git. Ricardo Wurmus2018-10-21
* gnu: tophat: Update to 2.1.1.•••* 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. Ricardo Wurmus2018-10-21
* gnu: python2-dendropy: Disable failing test.•••* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable failing test. Ben Woodcroft2018-10-21
* gnu: bowtie: Update to 2.3.4.3.•••* 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. Ricardo Wurmus2018-10-20
* gnu: blast+: Use INVOKE and return #T unconditionally.•••* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus2018-10-20
* gnu: bedops: Update to 2.4.35.•••* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35. [source]: Fetch from git. Ricardo Wurmus2018-10-20
* gnu: bedops: Use INVOKE.•••* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE. Ricardo Wurmus2018-10-20
* gnu: bamm: Fetch from git and use INVOKE.•••* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git. [arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus2018-10-20
* gnu: aragorn: Use invoke and simplify.•••* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build phase; simplify install phase. Ricardo Wurmus2018-10-20
* gnu: clipper: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1. [source]: Fetch from git. [arguments]: Add fix-typo phase. Ricardo Wurmus2018-10-20
* gnu: python-pybedtools: Update to 0.7.10.•••* 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. Ricardo Wurmus2018-10-20
* gnu: Add bedtools-2.26.•••* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable. Ricardo Wurmus2018-10-20
* gnu: kallisto: Update to 0.44.0.•••* 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. Ricardo Wurmus2018-10-11
* gnu: Add filtlong.•••* gnu/packages/bioinformatics.scm (filtlong): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org> pimi2018-10-08
* gnu: Add ngless.•••* gnu/packages/bioinformatics.scm (ngless): New variable. Ricardo Wurmus2018-10-05
* gnu: bioruby: Update to 1.5.2.•••This works with Ruby 2.5. * gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2. Christopher Baines2018-10-05
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