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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>
2018-09-20gnu: rsem: Update to 1.3.1.Ricardo Wurmus
* 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.
2018-09-14gnu: Add python-hic2cool.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
2018-09-10Adjust all users of (gnu packages ldc) to use (gnu packages dlang).Leo Famulari
This is a followup to commit 98d6543f86d01486c2f6e808eedd97c601ba3e7a. * gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust accordingly.
2018-09-10gnu: Add python-pygenometracks.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
2018-09-10gnu: Add python-hicexplorer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
2018-09-10gnu: Add python-cooler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
2018-09-10gnu: Add python-pyfaidx.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
2018-09-10gnu: Add python-pypairix.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
2018-09-10gnu: Add python-intervaltree.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
2018-09-09gnu: r-annotationhub: Update to 2.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
2018-09-06Add missing use-modules clause.Ricardo Wurmus
This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor).
2018-09-05gnu: pigx-scrnaseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-bsseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-chipseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-rnaseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
2018-09-05gnu: r-graph: Move from bioinformatics to bioconductor.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-graph): Move from here... * gnu/packages/bioconductor.scm (r-graph): ...to here.
2018-09-05gnu: r-scran: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
2018-09-05gnu: r-scater: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
2018-09-05gnu: r-hdf5array: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
2018-09-05gnu: r-ggbio: Update to 1.28.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5. [propagated-inputs]: Add r-rlang.
2018-09-05gnu: r-biovizbase: Update to 1.28.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2. [propagated-inputs]: Add r-rlang.
2018-09-05gnu: r-keggrest: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
2018-09-05gnu: r-edaseq: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
2018-09-05gnu: r-seurat: Update to 2.3.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4. [source]: Remove snippet. [arguments]: Remove. [native-inputs]: Remove. [propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger, r-stringr, r-tclust, and rvgam; add r-httr.
2018-09-05gnu: r-msnbase: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
2018-09-05gnu: r-maldiquant: Update to 1.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
2018-09-05gnu: r-seqminer: Update to 6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
2018-09-05gnu: r-genomicfeatures: Update to 1.32.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
2018-09-05gnu: r-rtracklayer: Update to 1.40.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
2018-09-05gnu: r-delayedarray: Update to 0.6.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
2018-09-05gnu: r-rsamtools: Update to 1.32.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
2018-09-05gnu: r-biocparallel: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
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