| Age | Commit message (Expand) | Author |
|---|
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | gnu: fasttree: Use INVOKE.•••* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify
install phase.
| Ricardo Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | gnu: eigensoft: Update to 7.2.1.•••* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1.
[arguments]: Remove Makefile modification.
| Ricardo Wurmus |
| 2018-10-21 | gnu: discrover: Fetch from git.•••* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | gnu: diamond: Fetch from git.•••* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | gnu: deeptools: Update to 3.1.3.•••* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
| Ricardo Wurmus |
| 2018-10-21 | gnu: python-dendropy: Fetch from git.•••* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | gnu: python-py2bit: Update to 0.3.0.•••* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
| Ricardo Wurmus |
| 2018-10-21 | gnu: cutadapt: Update to 1.18.•••* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18.
[inputs]: Add python-dnaio.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add python-dnaio.•••* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
| Ricardo Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | gnu: python-twobitreader: Update to 3.1.6.•••* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6.
[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | gnu: bwa-pssm: Fetch from git.•••* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | 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 Wurmus |
| 2018-10-21 | gnu: python2-dendropy: Disable failing test.•••* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
| Ben Woodcroft |
| 2018-10-20 | 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 |
| 2018-10-11 | 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 |
| 2018-10-08 | 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 |
