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* Merge branch 'master' into core-updatesMarius Bakke2020-04-131-2/+2
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| * gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to•••"efficiently obtains". * gnu/packages/bioinformatics (r-bamsignals): Fix grammar. Vagrant Cascadian2020-04-121-1/+1
| * gnu: r-qtl: Fix grammar "allows to estimate" to "estimates".•••* gnu/packages/bioinformatics (r-qtl): Fix grammar. Vagrant Cascadian2020-04-121-1/+1
* | Merge branch 'master' into core-updatesMarius Bakke2020-04-111-1/+1
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| * 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 Bakke2020-04-091-1/+1
* | Merge branch 'master' into core-updates••• Conflicts: etc/news.scm gnu/local.mk gnu/packages/check.scm gnu/packages/cross-base.scm gnu/packages/gimp.scm gnu/packages/java.scm gnu/packages/mail.scm gnu/packages/sdl.scm gnu/packages/texinfo.scm gnu/packages/tls.scm gnu/packages/version-control.scm Marius Bakke2020-04-081-8/+23
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| * 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 Kądziołka2020-04-051-4/+15
| * 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 Wurmus2020-04-011-2/+4
| * 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 Wurmus2020-04-011-2/+4
* | gnu: sailfish: Fix build failure.•••* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to CPLUS_INCLUDE_PATH instead of overriding it. Marius Bakke2020-04-031-1/+2
* | Merge branch 'master' into core-updates••• Conflicts: gnu/packages/icu4c.scm gnu/packages/man.scm gnu/packages/python-xyz.scm guix/scripts/environment.scm guix/scripts/pack.scm guix/scripts/package.scm guix/scripts/pull.scm guix/store.scm Marius Bakke2020-03-271-33/+110
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| * gnu: Update sambamba to 0.7.1.•••* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1; Remove unneeded undead input. Roel Janssen2020-03-261-19/+6
| * 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 Wurmus2020-03-241-2/+4
| * 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 Flashner2020-03-221-9/+46
| * 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 Flashner2020-03-221-3/+54
* | Merge branch 'master' into core-updatesMarius Bakke2020-03-181-5/+5
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| * gnu: pigx-scrnaseq: Update to 1.1.4.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4. Ricardo Wurmus2020-03-171-2/+2
| * gnu: star: Update to 2.7.3a.•••* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a. Ricardo Wurmus2020-03-161-3/+3
* | Merge branch 'master' into core-updatesMarius Bakke2020-03-141-12/+29
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| * gnu: edirect: Update to 13.3.20200128.•••* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128. [source]: Remove bundled certificate authority tarball. Efraim Flashner2020-03-121-2/+5
| * gnu: r-qtl: Update to 1.46-2.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2. Ricardo Wurmus2020-03-121-2/+2
| * 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 Flashner2020-03-111-3/+12
| * gnu: python-pyfaidx: Update to 0.5.8.•••* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8. Efraim Flashner2020-03-111-2/+2
| * gnu: Add python2-pyfaidx.•••* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable. Efraim Flashner2020-03-111-0/+3
| * 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 Höfling2020-03-101-3/+5
* | gnu: salmon: Adjust for C_INCLUDE_PATH changes.•••* gnu/packages/bioinformatics.scm (salmon)[arguments]: Append Eigen headers to C_INCLUDE_PATH instead of CPATH. Marius Bakke2020-03-131-2/+2
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* 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 Janssen2020-03-091-0/+2
* gnu: ngless: Update to 1.1.0.•••* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0. Ricardo Wurmus2020-03-081-2/+2
* 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 Wurmus2020-03-081-17/+42
* gnu: r-methylkit: Add r-knitr.•••* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr. Ricardo Wurmus2020-03-071-0/+2
* gnu: r-vsn: Add r-knitr.•••* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr. Ricardo Wurmus2020-03-071-0/+2
* 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 Wurmus2020-03-061-10/+11
* gnu: gess: Use WRAP-SCRIPT.•••* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT. [inputs]: Add guile-3.0 for wrapper. Ricardo Wurmus2020-03-031-2/+3
* gnu: gess: Override PYTHONPATH.•••* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH instead of augmenting it. Ricardo Wurmus2020-03-031-1/+1
* gnu: r-seqminer: Update to 8.0.•••* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0. Ricardo Wurmus2020-03-021-2/+2
* gnu: r-hdf5array: Update to 1.14.3.•••* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3. Ricardo Wurmus2020-03-011-2/+2
* gnu: r-rsamtools: Update to 2.2.3.•••* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3. Ricardo Wurmus2020-03-011-2/+2
* gnu: r-edger: Update to 3.28.1.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1. Ricardo Wurmus2020-03-011-2/+2
* 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 Wurmus2020-03-011-2/+3
* gnu: infernal: Update to 1.1.3.•••* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3. [native-inputs]: Add python. Ricardo Wurmus2020-02-271-4/+5
* gnu: vcftools: Update to 0.1.16.•••* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16. Ricardo Wurmus2020-02-271-2/+2
* 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 Wurmus2020-02-271-4/+5
* 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 Wurmus2020-02-271-19/+9
* 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 Wurmus2020-02-261-19/+33
* gnu: diamond: Update to 0.9.30.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30. Ricardo Wurmus2020-02-261-2/+2
* 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 Wurmus2020-02-261-8/+8
* 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 Wurmus2020-02-261-7/+18
* gnu: Remove python-loompy-for-pigx-scrnaseq.•••* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove variable. Ricardo Wurmus2020-02-261-17/+0
* 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 Wurmus2020-02-261-11/+6
* gnu: jamm: Update to 1.0.7.6.•••* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6. Ricardo Wurmus2020-02-251-2/+2
generated by cgit v1.2.3 (git 2.47.1) at 2025-01-24 18:16:16 +0000