| Age | Commit message (Expand) | Author |
|---|
| 2018-10-08 | gnu: Add filtlong....* gnu/packages/bioinformatics.scm (filtlong): New variable.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
| pimi |
| 2018-10-05 | gnu: Add ngless....* gnu/packages/bioinformatics.scm (ngless): New variable.
| Ricardo Wurmus |
| 2018-10-05 | gnu: bioruby: Update to 1.5.2....This works with Ruby 2.5.
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
| Christopher Baines |
| 2018-10-05 | gnu: samtools-0.1: Adjust to match changes in samtools....* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make
flags.
| Ricardo Wurmus |
| 2018-10-05 | gnu: deeptools: Update to 3.1.2....* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2.
[source]: Fetch from git.
[arguments]: Delete reset-gzip-timestamps phase.
[inputs]: Add python-plotly.
| Ricardo Wurmus |
| 2018-10-05 | gnu: python-pysam: Update to 0.15.1....* 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.
| Ricardo Wurmus |
| 2018-10-05 | gnu: bcftools: Update to 1.9....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9.
[arguments]: Remove obsolete make flags.
| Ricardo Wurmus |
| 2018-10-05 | gnu: samtools: Update to 1.9....* gnu/packages/bioinformatics.scm (samtools): Update to 1.9.
[origin]: Remove bundled htslib sources.
[arguments]: Remove obsolete make-flags.
| Ricardo Wurmus |
| 2018-10-05 | gnu: htslib: Update to 1.9....* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
| Ricardo Wurmus |
| 2018-10-02 | gnu: Add r-absfiltergsea....* gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.
| pimi |
| 2018-10-02 | gnu: Add poretools....* gnu/packages/bioinformatics.scm (poretools): New variable.
| pimi |
| 2018-09-30 | gnu: Add porechop....* gnu/packages/bioinformatics.scm (porechop): New variable.
| pimi |
| 2018-09-24 | gnu: Add r-bseqsc....* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
| Ricardo Wurmus |
| 2018-09-24 | gnu: Add r-cssam....* gnu/packages/bioinformatics.scm (r-cssam): New variable.
| Ricardo Wurmus |
| 2018-09-24 | gnu: Add r-xbioc....* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
| Ricardo Wurmus |
| 2018-09-22 | gnu: hmmer: Update to 3.2.1....* 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.
| Ben Woodcroft |
| 2018-09-21 | gnu: Add r-pore....* gnu/packages/bioinformatics.scm (r-pore): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| pimi |
| 2018-09-20 | gnu: rsem: Update to 1.3.1....* 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.
| Ricardo Wurmus |
| 2018-09-14 | gnu: Add python-hic2cool....* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
| Ricardo Wurmus |
| 2018-09-10 | Adjust all users of (gnu packages ldc) to use (gnu packages dlang)....This is a followup to commit 98d6543f86d01486c2f6e808eedd97c601ba3e7a.
* gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust
accordingly.
| Leo Famulari |
| 2018-09-10 | gnu: Add python-pygenometracks....* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-hicexplorer....* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-cooler....* gnu/packages/bioinformatics.scm (python-cooler): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-pyfaidx....* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-pypairix....* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-intervaltree....* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
| Ricardo Wurmus |
| 2018-09-09 | gnu: r-annotationhub: Update to 2.12.1....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
| Ricardo Wurmus |
| 2018-09-06 | Add missing use-modules clause....This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2.
Sorry!
* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-scrnaseq: Use latest version of Pandoc....* 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".
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-bsseq: Use latest version of Pandoc....* 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".
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-chipseq: Use latest version of Pandoc....* 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".
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-rnaseq: Use latest version of Pandoc....* 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".
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-rcas: Use standard version of ghc-pandoc-citeproc....* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-graph: Move from bioinformatics to bioconductor....* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-scran: Update to 1.8.4....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-scater: Update to 1.8.4....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-hdf5array: Update to 1.8.1....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-ggbio: Update to 1.28.5....* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-biovizbase: Update to 1.28.2....* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-keggrest: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-edaseq: Update to 2.14.1....* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-seurat: Update to 2.3.4....* 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.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-msnbase: Update to 2.6.3....* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-maldiquant: Update to 1.18....* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-seqminer: Update to 6.1....* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-genomicfeatures: Update to 1.32.2....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-rtracklayer: Update to 1.40.6....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-delayedarray: Update to 0.6.5....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-rsamtools: Update to 1.32.3....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-biocparallel: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
| Ricardo Wurmus |
