Age | Commit message (Collapse) | Author |
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"efficiently obtains".
* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
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* gnu/packages/bioinformatics (r-qtl): Fix grammar.
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* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
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* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
Remove unneeded undead input.
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* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
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* 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.
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* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
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* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
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* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
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* 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.
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* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
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* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
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* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
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* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to
native-inputs to make the test suite run succesfully.
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* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
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* 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.
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* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
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* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
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* 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.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
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* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
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* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
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* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
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* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
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* 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.
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* 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+
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
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* 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.
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* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
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* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
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* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
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