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2020-12-09gnu: r-genomeinfodb: Update to 1.26.0.zimoun
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.0.
2020-12-09gnu: r-bioccheck: Update to 1.26.0.zimoun
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.26.0.
2020-12-09gnu: r-biocstyle: Update to 2.18.0.zimoun
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.0.
2020-12-09gnu: r-biocviews: Update to 1.58.0.zimoun
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.0.
2020-12-09gnu: r-grohmm: Update to 1.24.0.zimoun
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.24.0.
2020-12-09gnu: r-systempiper: Update to 1.24.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.2. [propagated-inputs]: Add r-iranges.
2020-12-09gnu: r-shortread: Update to 1.48.0.zimoun
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.48.0.
2020-12-09gnu: r-gostats: Update to 2.56.0.zimoun
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.56.0.
2020-12-09gnu: r-category: Update to 2.56.0.zimoun
* gnu/packages/bioinformatics.scm (r-category): Update to 2.56.0.
2020-12-09gnu: r-gseabase: Update to 1.52.0.zimoun
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.0.
2020-12-09gnu: r-rbgl: Update to 1.66.0.zimoun
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.66.0.
2020-12-09gnu: r-annotationforge: Update to 1.32.0.zimoun
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.32.0.
2020-12-09gnu: r-dexseq: Update to 1.36.0.zimoun
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.36.0.
2020-12-09gnu: r-deseq2: Update to 1.30.0.zimoun
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.30.0.
2020-12-09gnu: r-genefilter: Update to 1.72.0.zimoun
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.0.
2020-12-09gnu: r-delayedarray: Update to 0.16.0.zimoun
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.0. [propagated-inputs]: Add r-matrixgenerics; remove r-matrixstats.
2020-12-09gnu: r-iranges: Update to 2.24.0.zimoun
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.0.
2020-12-09gnu: r-s4vectors: Update to 0.28.0.zimoun
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.0.
2020-12-09gnu: r-xvector: Update to 0.30.0.zimoun
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.30.0.
2020-12-09gnu: Update r-msnbase to 2.16.0.zimoun
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.0.
2020-12-07gnu: minimap2: Fix build on aarch64-linux.Efraim Flashner
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust configure-flags to be better per-architecture. [source]: Add patch. * gnu/packages/patches/minimap2-aarch64-support.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2020-12-07gnu: minimap2: Prepare for cross compilation.Efraim Flashner
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Use cc-for-target.
2020-12-01gnu: java-picard-1.113: Use ant/java8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use ant/java8. [inputs]: Replace ant with ant/java8.
2020-11-30gnu: pigx-chipseq: Update to 0.0.51.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.51. [inputs]: Add r-corrplot, r-deseq2, r-dt, r-ggrepel, r-gprofiler2, r-pheatmap, and r-rsubread.
2020-11-30gnu: pigx-scrnaseq: Update to 1.1.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.7.
2020-11-26Merge branch 'master' into stagingMarius Bakke
2020-11-24gnu: tadbit: Update to 1.0.1.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1. [arguments]: Remove #:tests? and #:python arguments. [phases]{fix-problems-with-setup.py}: Remove no longer needed steps. {check}: Override phase. [native-inputs]: Add glib and pkg-config. [inputs]: Add python-future and python-h5py.
2020-11-24gnu: imp: Migrate to Python 3.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (imp) [arguments]: Enable tests by removing the #:tests? argument. Specify the arguments to pass to the ctest test running via the #:configure-flags argument. [inputs]: Add cgal and opencv. Remove python-2. Move swig to... [native-inputs]: ...here. Add python-wrapper. [propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas, python2-scikit-learn and python2-networkx by python-numpy, python-scipy, python-pandas, python-scikit-learn and python-networkx, respectively.
2020-11-23Merge branch 'master' into stagingMarius Bakke
2020-11-23gnu: Add cwltool.Efraim Flashner
* gnu/packages/bioinformatics.scm (cwltool): New variable.
2020-11-23gnu: Add python-schema-salad.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
2020-11-15Merge branch 'master' into stagingMarius Bakke
2020-11-15gnu: methyldackel: Update to 0.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1. [arguments]: Link with libbigwig. [inputs]: Add curl and libbigwig; replace htslib with htslib-1.9.
2020-11-13gnu: Fix build for python-pysam.Roel Janssen
* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9, samtools-1.9, and bcftools-1.9.
2020-11-13gnu: Add bcftools-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
2020-11-13gnu: bedtools: Use samtools-1.9.Roel Janssen
The build for bedtools with samtools 1.11 triggers a testsuite failure which is reported here: https://github.com/arq5x/bedtools2/issues/814 * gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
2020-11-13gnu: Add samtools-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
2020-11-13gnu: Add htslib-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
2020-11-11Merge branch 'master' into stagingMarius Bakke
2020-11-09gnu: macs: Remove generated code.Efraim Flashner
* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove cython generated code. [native-inputs]: Add python-cython.
2020-11-09gnu: macs: Update check phase.Efraim Flashner
* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check phase before using custom 'check phase.
2020-11-09gnu: macs: Update source, home-page URIs.Efraim Flashner
* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update URIs to new location.
2020-11-07Merge branch 'master' into stagingMarius Bakke
Conflicts: gnu/local.mk gnu/packages/gdb.scm gnu/packages/lisp-xyz.scm gnu/packages/web-browsers.scm
2020-10-29gnu: Update samtools to 1.11.Roel Janssen
* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
2020-10-29gnu: Update bcftools to 1.11.Roel Janssen
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
2020-10-29gnu: Update htslib to 1.11.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
2020-10-23gnu: imp: Update to 2.13.0.Ludovic Courtès
* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0.
2020-10-13gnu: Remove redundant MariaDB inputs.Marius Bakke
For well-behaved build systems, including the "dev" output suffices. * gnu/packages/bioinformatics.scm (kentutils)[inputs]: Remove MARIADB:LIB. * gnu/packages/cran.scm (r-rmysql)[inputs]: Likewise. * gnu/packages/databases.scm (python-mysqlclient, soci)[inputs]: Likewise. * gnu/packages/qt.scm (qt-4, qtbase): Likewise. * gnu/packages/ruby.scm (ruby-mysql2)[inputs]: Likewise.
2020-10-13Merge branch 'master' into stagingMarius Bakke
2020-10-07gnu: htslib: Enable support for custom URI schemes.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.
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