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path: root/gnu/packages/bioinformatics.scm
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2020-03-18Merge branch 'master' into core-updatesMarius Bakke
2020-03-14Merge branch 'master' into core-updatesMarius Bakke
2020-03-17gnu: pigx-scrnaseq: Update to 1.1.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
2020-03-16gnu: star: Update to 2.7.3a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
2020-03-13gnu: salmon: Adjust for C_INCLUDE_PATH changes.Marius Bakke
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Append Eigen headers to C_INCLUDE_PATH instead of CPATH.
2020-03-12gnu: edirect: Update to 13.3.20200128.Efraim Flashner
* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128. [source]: Remove bundled certificate authority tarball.
2020-03-12gnu: r-qtl: Update to 1.46-2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
2020-03-11gnu: python-pybedtools: Update to 0.8.1.Efraim Flashner
* 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.
2020-03-11gnu: python-pyfaidx: Update to 0.5.8.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
2020-03-11gnu: Add python2-pyfaidx.Efraim Flashner
* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
2020-03-10gnu: java-forester-1.005: Update source URI.Björn Höfling
* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI. [native-inputs]: Wrap long line.
2020-03-09gnu: Fix build of python-velocyto.Roel Janssen
* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to native-inputs to make the test suite run succesfully.
2020-03-08gnu: ngless: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
2020-03-08gnu: taxtastic: Update to 0.8.11.Ricardo Wurmus
* 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.
2020-03-07gnu: r-methylkit: Add r-knitr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
2020-03-07gnu: r-vsn: Add r-knitr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
2020-03-06gnu: python-scanpy: Update to 1.4.5.1.Ricardo Wurmus
* 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.
2020-03-03gnu: gess: Use WRAP-SCRIPT.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT. [inputs]: Add guile-3.0 for wrapper.
2020-03-03gnu: gess: Override PYTHONPATH.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH instead of augmenting it.
2020-03-02gnu: r-seqminer: Update to 8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
2020-03-01gnu: r-hdf5array: Update to 1.14.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
2020-03-01gnu: r-rsamtools: Update to 2.2.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
2020-03-01gnu: r-edger: Update to 3.28.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
2020-03-01gnu: r-seurat: Update to 3.1.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4. [propagated-inputs]: Add r-patchwork.
2020-02-27gnu: infernal: Update to 1.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3. [native-inputs]: Add python.
2020-02-27gnu: vcftools: Update to 0.1.16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
2020-02-27gnu: bedtools: Update to 2.29.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2. [native-inputs]: Replace python-2 with python-wrapper. [license]: Change to Expat.
2020-02-27gnu: rseqc: Update to 3.0.1.Ricardo Wurmus
* 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.
2020-02-26gnu: proteinortho: Update to 6.0.14.Ricardo Wurmus
* 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+
2020-02-26gnu: diamond: Update to 0.9.30.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
2020-02-26gnu: crossmap: Update to 0.3.8.Ricardo Wurmus
* 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.
2020-02-26gnu: macs: Update to 2.2.6.Ricardo Wurmus
* 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.
2020-02-26gnu: Remove python-loompy-for-pigx-scrnaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove variable.
2020-02-26gnu: pigx-scrnaseq: Update to 1.1.3.Ricardo Wurmus
* 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.
2020-02-25gnu: jamm: Update to 1.0.7.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
2020-02-19gnu: r-scran: Update to 1.14.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
2020-02-19gnu: r-hdf5array: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
2020-02-19gnu: r-gviz: Update to 1.30.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
2020-02-19gnu: r-rhtslib: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
2020-02-19gnu: r-genomicfeatures: Update to 1.38.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
2020-02-19gnu: r-rsamtools: Update to 2.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
2020-02-19gnu: r-limma: Update to 3.42.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
2020-02-19gnu: r-shortread: Update to 1.44.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
2020-02-19gnu: r-seurat: Update to 3.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3. [propagated-inputs]: Remove r-sdmtools.
2020-02-19gnu: r-qtl: Update to 1.45-11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
2020-02-18gn: edirect: Update to 12.1.20190829.Efraim Flashner
The previous version has disappeared upstream. * gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
2020-02-13gnu: python2-pbcore: Remove python2-sphinx dependency.Marius Bakke
* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases. [native-inputs]: Remove PYTHON2-SPHINX.
2020-01-27gnu: r-gviz: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
2020-01-27gnu: r-genomicfeatures: Update to 1.38.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
2020-01-27gnu: r-s4vectors: Update to 0.24.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
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