| Age | Commit message (Expand) | Author |
|---|
| 2020-04-26 | gnu: python-scanpy: Update to 1.4.6....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
| Efraim Flashner |
| 2020-04-17 | gnu: python-pygenometracks: Update to 3.3....* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.3.
[arguments]: Add phase "relax-requirements"; disable tests.
[propagated-inputs]: Remove python-configparser and python-hicexplorer; add
python-gffutils, python-pysam, and python-tqdm.
| Ricardo Wurmus |
| 2020-04-17 | gnu: Add python-hicmatrix....* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
| Ricardo Wurmus |
| 2020-04-17 | gnu: python-cooler: Update to 0.8.7....* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.7.
[propagated-inputs]: Add python-asciitree, python-numpy, python-pyyaml, and
python-simplejson.
[native-inputs]: Remove python-nose, python-numpydoc, and python-sphinx; add
python-pytest.
| Ricardo Wurmus |
| 2020-04-17 | gnu: python-pybigwig: Update to 0.3.17....* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
| Ricardo Wurmus |
| 2020-04-14 | gnu: r-delayedarray: Update to 0.12.3....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-04-14 | gnu: r-s4vectors: Update to 0.24.4....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.
| Ricardo Wurmus |
| 2020-04-14 | gnu: pigx-chipseq: Update to 0.0.42....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42.
| Ricardo Wurmus |
| 2020-04-12 | gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to..."efficiently obtains".
* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
| Vagrant Cascadian |
| 2020-04-12 | gnu: r-qtl: Fix grammar "allows to estimate" to "estimates"....* gnu/packages/bioinformatics (r-qtl): Fix grammar.
| Vagrant Cascadian |
| 2020-04-09 | gnu: minimap2: Fix cond expression for Guile 3 compatibility....* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
| Marius Bakke |
| 2020-04-05 | gnu: python-intervaltree: Update to 3.0.2....* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
| Jakub Kądziołka |
| 2020-04-01 | gnu: r-biomart: Update to 2.42.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-04-01 | gnu: r-genomeinfodb: Update to 1.22.1....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-26 | gnu: Update sambamba to 0.7.1....* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
Remove unneeded undead input.
| Roel Janssen |
| 2020-03-24 | gnu: r-tximport: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-22 | gnu: edirect: Install more programs....* gnu/packages/bioinformatics.scm (edirect)[arguments]: Add
'patch-programs phase to work around not finding binaries in the PATH.
Rewrite 'install phase to install many more scripts. Rewrite
'wrap-program to wrap more scripts with more programs.
[inputs]: Add edirect-go-programs.
[native-search-paths]: New field.
| Efraim Flashner |
| 2020-03-22 | gnu: Add edirect-go-programs....* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
| Efraim Flashner |
| 2020-03-17 | gnu: pigx-scrnaseq: Update to 1.1.4....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
| Ricardo Wurmus |
| 2020-03-16 | gnu: star: Update to 2.7.3a....* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
| Ricardo Wurmus |
| 2020-03-12 | gnu: edirect: Update to 13.3.20200128....* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
| Efraim Flashner |
| 2020-03-12 | gnu: r-qtl: Update to 1.46-2....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
| Ricardo Wurmus |
| 2020-03-11 | gnu: python-pybedtools: Update to 0.8.1....* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
| Efraim Flashner |
| 2020-03-11 | gnu: python-pyfaidx: Update to 0.5.8....* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
| Efraim Flashner |
| 2020-03-11 | gnu: Add python2-pyfaidx....* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
| Efraim Flashner |
| 2020-03-10 | gnu: java-forester-1.005: Update source URI....* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
| Björn Höfling |
| 2020-03-09 | gnu: Fix build of python-velocyto....* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to
native-inputs to make the test suite run succesfully.
| Roel Janssen |
| 2020-03-08 | gnu: ngless: Update to 1.1.0....* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
| Ricardo Wurmus |
| 2020-03-08 | gnu: taxtastic: Update to 0.8.11....* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11.
[source]: Fetch from Github.
[arguments]: Build with default Python; add phases 'prepare-directory,
'python37-compatibility, and update 'check phase.
[propagated-inputs]: Replace Python 2 variants with Python 3 variants.
| Ricardo Wurmus |
| 2020-03-07 | gnu: r-methylkit: Add r-knitr....* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-07 | gnu: r-vsn: Add r-knitr....* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-06 | gnu: python-scanpy: Update to 1.4.5.1....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.5.1.
[source]: Fetch from pypi.
[propagated-inputs]: Add python-legacy-api-wrap, python-packaging,
python-patsy, and python-umap-learn.
[native-inputs]: Add python-setuptools-scm.
| Ricardo Wurmus |
| 2020-03-03 | gnu: gess: Use WRAP-SCRIPT....* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
| Ricardo Wurmus |
| 2020-03-03 | gnu: gess: Override PYTHONPATH....* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
| Ricardo Wurmus |
| 2020-03-02 | gnu: r-seqminer: Update to 8.0....* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-hdf5array: Update to 1.14.3....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-rsamtools: Update to 2.2.3....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-edger: Update to 3.28.1....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-seurat: Update to 3.1.4....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
| Ricardo Wurmus |
| 2020-02-27 | gnu: infernal: Update to 1.1.3....* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
| Ricardo Wurmus |
| 2020-02-27 | gnu: vcftools: Update to 0.1.16....* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
| Ricardo Wurmus |
| 2020-02-27 | gnu: bedtools: Update to 2.29.2....* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
| Ricardo Wurmus |
| 2020-02-27 | gnu: rseqc: Update to 3.0.1....* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
| Ricardo Wurmus |
| 2020-02-26 | gnu: proteinortho: Update to 6.0.14....* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
| Ricardo Wurmus |
| 2020-02-26 | gnu: diamond: Update to 0.9.30....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
| Ricardo Wurmus |
| 2020-02-26 | gnu: crossmap: Update to 0.3.8....* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8.
[arguments]: Remove to build with default Python.
[inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and
python2-pysam with their Python 3 variants.
[native-inputs]: Replace python2-cython and python2-nose with their Python 3
variants.
| Ricardo Wurmus |
| 2020-02-26 | gnu: macs: Update to 2.2.6....* gnu/packages/bioinformatics.scm (macs): Update to 2.2.6.
[source]: Fetch from git.
[arguments]: Enable tests, build with default Python.
[inputs]: Replace python2-numpy with python-numpy.
[native-inputs]: Add python-pytest.
| Ricardo Wurmus |
| 2020-02-26 | gnu: Remove python-loompy-for-pigx-scrnaseq....* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
| Ricardo Wurmus |
| 2020-02-26 | gnu: pigx-scrnaseq: Update to 1.1.3....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3.
[arguments]: Remove.
[inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and
r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
| Ricardo Wurmus |
| 2020-02-25 | gnu: jamm: Update to 1.0.7.6....* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
| Ricardo Wurmus |
