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* gnu: python2-dendropy: Disable failing test.Ben Woodcroft2018-10-21
| | | | | * gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable failing test.
* gnu: bowtie: Update to 2.3.4.3.Ricardo Wurmus2018-10-20
| | | | | | | | | * 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.
* gnu: blast+: Use INVOKE and return #T unconditionally.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: bedops: Update to 2.4.35.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35. [source]: Fetch from git.
* gnu: bedops: Use INVOKE.Ricardo Wurmus2018-10-20
| | | | * gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
* gnu: bamm: Fetch from git and use INVOKE.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git. [arguments]: Use INVOKE and return #T unconditionally.
* gnu: aragorn: Use invoke and simplify.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build phase; simplify install phase.
* gnu: clipper: Update to 1.2.1.Ricardo Wurmus2018-10-20
| | | | | | * gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1. [source]: Fetch from git. [arguments]: Add fix-typo phase.
* gnu: python-pybedtools: Update to 0.7.10.Ricardo Wurmus2018-10-20
| | | | | | | | | | * 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.
* gnu: Add bedtools-2.26.Ricardo Wurmus2018-10-20
| | | | * gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
* gnu: kallisto: Update to 0.44.0.Ricardo Wurmus2018-10-11
| | | | | | | * 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.
* gnu: Add filtlong.pimi2018-10-08
| | | | | | * gnu/packages/bioinformatics.scm (filtlong): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add ngless.Ricardo Wurmus2018-10-05
| | | | * gnu/packages/bioinformatics.scm (ngless): New variable.
* gnu: bioruby: Update to 1.5.2.Christopher Baines2018-10-05
| | | | | | This works with Ruby 2.5. * gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
* gnu: samtools-0.1: Adjust to match changes in samtools.Ricardo Wurmus2018-10-05
| | | | | * gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make flags.
* gnu: deeptools: Update to 3.1.2.Ricardo Wurmus2018-10-05
| | | | | | | * gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2. [source]: Fetch from git. [arguments]: Delete reset-gzip-timestamps phase. [inputs]: Add python-plotly.
* gnu: python-pysam: Update to 0.15.1.Ricardo Wurmus2018-10-05
| | | | | | | * 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.
* gnu: bcftools: Update to 1.9.Ricardo Wurmus2018-10-05
| | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.9. [arguments]: Remove obsolete make flags.
* gnu: samtools: Update to 1.9.Ricardo Wurmus2018-10-05
| | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.9. [origin]: Remove bundled htslib sources. [arguments]: Remove obsolete make-flags.
* gnu: htslib: Update to 1.9.Ricardo Wurmus2018-10-05
| | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
* gnu: Add r-absfiltergsea.pimi2018-10-02
| | | | * gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.
* gnu: Add poretools.pimi2018-10-02
| | | | * gnu/packages/bioinformatics.scm (poretools): New variable.
* gnu: Add porechop.pimi2018-09-30
| | | | * gnu/packages/bioinformatics.scm (porechop): New variable.
* gnu: Add r-bseqsc.Ricardo Wurmus2018-09-24
| | | | * gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
* gnu: Add r-cssam.Ricardo Wurmus2018-09-24
| | | | * gnu/packages/bioinformatics.scm (r-cssam): New variable.
* gnu: Add r-xbioc.Ricardo Wurmus2018-09-24
| | | | * gnu/packages/bioinformatics.scm (r-xbioc): New variable.
* gnu: hmmer: Update to 3.2.1.Ben Woodcroft2018-09-22
| | | | | | | | | * 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.
* gnu: Add r-pore.pimi2018-09-21
| | | | | | * gnu/packages/bioinformatics.scm (r-pore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: rsem: Update to 1.3.1.Ricardo Wurmus2018-09-20
| | | | | | | | | * gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1. [source]: Fetch from git; remove patch; delete bundled samtools. [arguments]: Pass make flags; adjust phases. [inputs]: Remove ncurses and samtools-0.1; add htslib-1.3. * gnu/packages/patches/rsem-makefile.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: Add python-hic2cool.Ricardo Wurmus2018-09-14
| | | | * gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
* Adjust all users of (gnu packages ldc) to use (gnu packages dlang).Leo Famulari2018-09-10
| | | | | | | This is a followup to commit 98d6543f86d01486c2f6e808eedd97c601ba3e7a. * gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust accordingly.
* gnu: Add python-pygenometracks.Ricardo Wurmus2018-09-10
| | | | * gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
* gnu: Add python-hicexplorer.Ricardo Wurmus2018-09-10
| | | | * gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
* gnu: Add python-cooler.Ricardo Wurmus2018-09-10
| | | | * gnu/packages/bioinformatics.scm (python-cooler): New variable.
* gnu: Add python-pyfaidx.Ricardo Wurmus2018-09-10
| | | | * gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
* gnu: Add python-pypairix.Ricardo Wurmus2018-09-10
| | | | * gnu/packages/bioinformatics.scm (python-pypairix): New variable.
* gnu: Add python-intervaltree.Ricardo Wurmus2018-09-10
| | | | * gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
* gnu: r-annotationhub: Update to 2.12.1.Ricardo Wurmus2018-09-09
| | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
* Add missing use-modules clause.Ricardo Wurmus2018-09-06
| | | | | | | | This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor).
* gnu: pigx-scrnaseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: pigx-bsseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: pigx-chipseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: pigx-rnaseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
* gnu: r-graph: Move from bioinformatics to bioconductor.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (r-graph): Move from here... * gnu/packages/bioconductor.scm (r-graph): ...to here.
* gnu: r-scran: Update to 1.8.4.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
* gnu: r-scater: Update to 1.8.4.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
* gnu: r-hdf5array: Update to 1.8.1.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
* gnu: r-ggbio: Update to 1.28.5.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5. [propagated-inputs]: Add r-rlang.
* gnu: r-biovizbase: Update to 1.28.2.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2. [propagated-inputs]: Add r-rlang.
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