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2020-06-06gnu: rcas-web: Use guile2.2 version of Guile-Redis....* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change from GUILE-REDIS to GUILE2.2-REDIS. While at it, rename the GUILE input to "guile" instead of "guile-next". Marius Bakke
2020-06-04gnu: 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 Wurmus
2020-06-03gnu: Add python-pairtools....* gnu/packages/bioinformatics.scm (python-pairtools): New variable. Ricardo Wurmus
2020-06-03gnu: Remove bedtools-2.26....* gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable. Ricardo Wurmus
2020-06-03gnu: 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 Wurmus
2020-05-27gnu: blast+: Use HTTPS home page URI....* gnu/packages/bioinformatics.scm (blast+)[home-page]: Use HTTPS URI. Nicolas Goaziou
2020-05-27gnu: bbmap: Use HTTPS home page URI....* gnu/packages/bioinformatics.scm (bbmap)[home-page]: Use HTTPS URI. Nicolas Goaziou
2020-05-19gnu: 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 Wurmus
2020-05-19gnu: ncbi-vdb: Update to 2.10.6....* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.10.6. Ricardo Wurmus
2020-05-19gnu: ngs-sdk: Update to 2.10.5....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.10.5. Ricardo Wurmus
2020-05-05Merge branch 'master' into core-updatesMarius Bakke
2020-05-05gnu: 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 Flashner
2020-04-30Merge 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 Bakke
2020-04-30gnu: Add miniasm....* gnu/packages/bioinformatics.scm (miniasm): New variable. Roel Janssen
2020-04-30gnu: python2-warpedlmm: Fix build....* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add python2-weave. [arguments]: Disable tests and add "use-weave" phase. Ricardo Wurmus
2020-04-28gnu: Add variant-tools....* gnu/packages/bioinformatics.scm (variant-tools): New variable. Ricardo Wurmus
2020-04-28gnu: r-hdf5array: Update to 1.14.4....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4. Ricardo Wurmus
2020-04-28gnu: r-seurat: Update to 3.1.5....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5. [propagated-inputs]: Remove r-metap. Ricardo Wurmus
2020-04-27gnu: Update minimap2 to 2.17....* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17. Roel Janssen
2020-04-27gnu: Add python-deeptools....* gnu/packages/bioinformatics.scm (python-deeptools): New variable. Roel Janssen
2020-04-27gnu: Add python-deeptoolsintervals....* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable. Roel Janssen
2020-04-26gnu: 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 Flashner
2020-04-19Merge branch 'master' into core-updatesMarius Bakke
2020-04-17gnu: 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 Wurmus
2020-04-17gnu: Add python-hicmatrix....* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable. Ricardo Wurmus
2020-04-17gnu: 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 Wurmus
2020-04-17gnu: python-pybigwig: Update to 0.3.17....* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17. Ricardo Wurmus
2020-04-15Merge branch 'master' into core-updatesMarius Bakke
2020-04-14gnu: r-delayedarray: Update to 0.12.3....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-04-14gnu: r-s4vectors: Update to 0.24.4....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4. Ricardo Wurmus
2020-04-14gnu: pigx-chipseq: Update to 0.0.42....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42. Ricardo Wurmus
2020-04-13Merge branch 'master' into core-updatesMarius Bakke
2020-04-12gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to..."efficiently obtains". * gnu/packages/bioinformatics (r-bamsignals): Fix grammar. Vagrant Cascadian
2020-04-12gnu: r-qtl: Fix grammar "allows to estimate" to "estimates"....* gnu/packages/bioinformatics (r-qtl): Fix grammar. Vagrant Cascadian
2020-04-11Merge branch 'master' into core-updatesMarius Bakke
2020-04-09gnu: 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 Bakke
2020-04-08Merge 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 Bakke
2020-04-05gnu: 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 Kądziołka
2020-04-03gnu: sailfish: Fix build failure....* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to CPLUS_INCLUDE_PATH instead of overriding it. Marius Bakke
2020-04-01gnu: r-biomart: Update to 2.42.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-04-01gnu: r-genomeinfodb: Update to 1.22.1....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-03-27Merge 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 Bakke
2020-03-26gnu: Update sambamba to 0.7.1....* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1; Remove unneeded undead input. Roel Janssen
2020-03-24gnu: r-tximport: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-03-22gnu: 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 Flashner
2020-03-22gnu: Add edirect-go-programs....* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable. (edirect)[source]: Adjust snippet to not use non-free software. Efraim Flashner
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....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4. Ricardo Wurmus
2020-03-16gnu: star: Update to 2.7.3a....* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a. Ricardo Wurmus
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