| Commit message (Expand) | Author | Age |
|---|
| * | gnu: python2-dendropy: Disable failing test.•••* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
| Ben Woodcroft | 2018-10-21 |
| * | 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 Wurmus | 2018-10-20 |
| * | gnu: blast+: Use INVOKE and return #T unconditionally.•••* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus | 2018-10-20 |
| * | gnu: bedops: Update to 2.4.35.•••* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
| Ricardo Wurmus | 2018-10-20 |
| * | gnu: bedops: Use INVOKE.•••* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
| Ricardo Wurmus | 2018-10-20 |
| * | 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 Wurmus | 2018-10-20 |
| * | gnu: aragorn: Use invoke and simplify.•••* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
| Ricardo Wurmus | 2018-10-20 |
| * | 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 Wurmus | 2018-10-20 |
| * | 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 Wurmus | 2018-10-20 |
| * | gnu: Add bedtools-2.26.•••* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
| Ricardo Wurmus | 2018-10-20 |
| * | 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 Wurmus | 2018-10-11 |
| * | gnu: Add filtlong.•••* gnu/packages/bioinformatics.scm (filtlong): New variable.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
| pimi | 2018-10-08 |
| * | 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 | 2018-10-05 |
| * | 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 | 2018-10-02 |
| * | gnu: Add porechop.•••* gnu/packages/bioinformatics.scm (porechop): New variable.
| pimi | 2018-09-30 |
| * | 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 | 2018-09-24 |
| * | 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 | 2018-09-22 |
| * | gnu: Add r-pore.•••* gnu/packages/bioinformatics.scm (r-pore): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| pimi | 2018-09-21 |
| * | 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 | 2018-09-20 |
| * | gnu: Add python-hic2cool.•••* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
| Ricardo Wurmus | 2018-09-14 |
| * | 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 | 2018-09-10 |
| * | gnu: r-annotationhub: Update to 2.12.1.•••* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
| Ricardo Wurmus | 2018-09-09 |
| * | 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 | 2018-09-06 |
| * | 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 |