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* gnu: python-pypairix: Update to 0.3.7 and build programs.•••* gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.7. [source]: Fetch from github. [arguments]: Add phases "build-programs" and "install-programs". Ricardo Wurmus2020-06-04
* gnu: Add python-pairtools.•••* gnu/packages/bioinformatics.scm (python-pairtools): New variable. Ricardo Wurmus2020-06-03
* gnu: Remove bedtools-2.26.•••* gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable. Ricardo Wurmus2020-06-03
* gnu: python-pybedtools: Disable unreliable test.•••* gnu/packages/bioinformatics.scm (python-pybedtools)[arguments]: Disable test_intron_exon_reads test; run tests verbosely. test_intron_exon_reads Ricardo Wurmus2020-06-03
* gnu: blast+: Use HTTPS home page URI.•••* gnu/packages/bioinformatics.scm (blast+)[home-page]: Use HTTPS URI. Nicolas Goaziou2020-05-27
* gnu: bbmap: Use HTTPS home page URI.•••* gnu/packages/bioinformatics.scm (bbmap)[home-page]: Use HTTPS URI. Nicolas Goaziou2020-05-27
* gnu: sra-tools: Update to 2.10.6.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6. [arguments]: Replace CC variable in utf8proc Makefile. [inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper. Ricardo Wurmus2020-05-19
* gnu: ncbi-vdb: Update to 2.10.6.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.10.6. Ricardo Wurmus2020-05-19
* gnu: ngs-sdk: Update to 2.10.5.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.10.5. Ricardo Wurmus2020-05-19
* Merge branch 'master' into core-updatesMarius Bakke2020-05-05
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| * gnu: Add grocsvs.•••* 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. Efraim Flashner2020-05-05
* | Merge branch 'master' into core-updates••• 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 Marius Bakke2020-04-30
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| * gnu: Add miniasm.•••* gnu/packages/bioinformatics.scm (miniasm): New variable. Roel Janssen2020-04-30
| * gnu: python2-warpedlmm: Fix build.•••* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add python2-weave. [arguments]: Disable tests and add "use-weave" phase. Ricardo Wurmus2020-04-30
| * gnu: Add variant-tools.•••* gnu/packages/bioinformatics.scm (variant-tools): New variable. Ricardo Wurmus2020-04-28
| * gnu: r-hdf5array: Update to 1.14.4.•••* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4. Ricardo Wurmus2020-04-28
| * gnu: r-seurat: Update to 3.1.5.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5. [propagated-inputs]: Remove r-metap. Ricardo Wurmus2020-04-28
| * gnu: Update minimap2 to 2.17.•••* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17. Roel Janssen2020-04-27
| * gnu: Add python-deeptools.•••* gnu/packages/bioinformatics.scm (python-deeptools): New variable. Roel Janssen2020-04-27
| * gnu: Add python-deeptoolsintervals.•••* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable. Roel Janssen2020-04-27
| * 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 Flashner2020-04-26
* | Merge branch 'master' into core-updatesMarius Bakke2020-04-19
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| * 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 Wurmus2020-04-17
| * gnu: Add python-hicmatrix.•••* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable. Ricardo Wurmus2020-04-17
| * 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 Wurmus2020-04-17
| * gnu: python-pybigwig: Update to 0.3.17.•••* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17. Ricardo Wurmus2020-04-17
* | Merge branch 'master' into core-updatesMarius Bakke2020-04-15
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| * 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 Wurmus2020-04-14
| * gnu: r-s4vectors: Update to 0.24.4.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4. Ricardo Wurmus2020-04-14
| * gnu: pigx-chipseq: Update to 0.0.42.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42. Ricardo Wurmus2020-04-14
* | Merge branch 'master' into core-updatesMarius Bakke2020-04-13
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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 Cascadian2020-04-12
| * gnu: r-qtl: Fix grammar "allows to estimate" to "estimates".•••* gnu/packages/bioinformatics (r-qtl): Fix grammar. Vagrant Cascadian2020-04-12
* | Merge branch 'master' into core-updatesMarius Bakke2020-04-11
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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 Bakke2020-04-09
* | 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 Bakke2020-04-08
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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 Kądziołka2020-04-05
| * 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 Wurmus2020-04-01
| * 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 Wurmus2020-04-01
* | gnu: sailfish: Fix build failure.•••* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to CPLUS_INCLUDE_PATH instead of overriding it. Marius Bakke2020-04-03
* | 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 Bakke2020-03-27
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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 Janssen2020-03-26
| * 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 Wurmus2020-03-24
| * 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 Flashner2020-03-22
| * 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 Flashner2020-03-22
* | Merge branch 'master' into core-updatesMarius Bakke2020-03-18
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| * gnu: pigx-scrnaseq: Update to 1.1.4.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4. Ricardo Wurmus2020-03-17
| * gnu: star: Update to 2.7.3a.•••* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a. Ricardo Wurmus2020-03-16
* | Merge branch 'master' into core-updatesMarius Bakke2020-03-14
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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 Flashner2020-03-12
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