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2020-05-05Merge branch 'master' into core-updatesMarius Bakke
2020-05-05gnu: Add grocsvs.Efraim Flashner
* gnu/packages/bioinformatics.scm (grocsvs): New variable. * gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2020-04-30Merge branch 'master' into core-updatesMarius Bakke
Conflicts: gnu/local.mk gnu/packages/backup.scm gnu/packages/emacs-xyz.scm gnu/packages/guile.scm gnu/packages/lisp.scm gnu/packages/openldap.scm gnu/packages/package-management.scm gnu/packages/web.scm gnu/packages/xorg.scm
2020-04-30gnu: Add miniasm.Roel Janssen
* gnu/packages/bioinformatics.scm (miniasm): New variable.
2020-04-30gnu: python2-warpedlmm: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add python2-weave. [arguments]: Disable tests and add "use-weave" phase.
2020-04-28gnu: Add variant-tools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (variant-tools): New variable.
2020-04-28gnu: r-hdf5array: Update to 1.14.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
2020-04-28gnu: r-seurat: Update to 3.1.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5. [propagated-inputs]: Remove r-metap.
2020-04-27gnu: Update minimap2 to 2.17.Roel Janssen
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
2020-04-27gnu: Add python-deeptools.Roel Janssen
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
2020-04-27gnu: Add python-deeptoolsintervals.Roel Janssen
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
2020-04-26gnu: python-scanpy: Update to 1.4.6.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6. [arguments]: Add another network based test to skip. [propagated-inputs]: Add python-tqdm.
2020-04-19Merge branch 'master' into core-updatesMarius Bakke
2020-04-17gnu: python-pygenometracks: Update to 3.3.Ricardo Wurmus
* 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.
2020-04-17gnu: Add python-hicmatrix.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
2020-04-17gnu: python-cooler: Update to 0.8.7.Ricardo Wurmus
* 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.
2020-04-17gnu: python-pybigwig: Update to 0.3.17.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
2020-04-15Merge branch 'master' into core-updatesMarius Bakke
2020-04-14gnu: r-delayedarray: Update to 0.12.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3. [native-inputs]: Add r-knitr.
2020-04-14gnu: r-s4vectors: Update to 0.24.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.
2020-04-14gnu: pigx-chipseq: Update to 0.0.42.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42.
2020-04-13Merge branch 'master' into core-updatesMarius Bakke
2020-04-12gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" toVagrant Cascadian
"efficiently obtains". * gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
2020-04-12gnu: r-qtl: Fix grammar "allows to estimate" to "estimates".Vagrant Cascadian
* gnu/packages/bioinformatics (r-qtl): Fix grammar.
2020-04-11Merge branch 'master' into core-updatesMarius Bakke
2020-04-09gnu: minimap2: Fix cond expression for Guile 3 compatibility.Marius Bakke
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND test the symbol else instead of _.
2020-04-08Merge branch 'master' into core-updatesMarius Bakke
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
2020-04-05gnu: python-intervaltree: Update to 3.0.2.Jakub Kądziołka
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2. [arguments]: Don't skip the tests, work around the problematic sanity-check instead.
2020-04-03gnu: sailfish: Fix build failure.Marius Bakke
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to CPLUS_INCLUDE_PATH instead of overriding it.
2020-04-01gnu: r-biomart: Update to 2.42.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-genomeinfodb: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1. [native-inputs]: Add r-knitr.
2020-03-27Merge branch 'master' into core-updatesMarius Bakke
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
2020-03-26gnu: Update sambamba to 0.7.1.Roel Janssen
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1; Remove unneeded undead input.
2020-03-24gnu: r-tximport: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2. [native-inputs]: Add r-knitr.
2020-03-22gnu: edirect: Install more programs.Efraim Flashner
* 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.
2020-03-22gnu: Add edirect-go-programs.Efraim Flashner
* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable. (edirect)[source]: Adjust snippet to not use non-free software.
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.
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