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2017-12-19gnu: r-biomart: Update to 2.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1. [propagated-inputs]: Add r-httr.
2017-12-19gnu: r-gviz: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
2017-12-19gnu: r-gqtlstats: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
2017-12-19gnu: r-rtracklayer: Update to 1.38.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
2017-12-19gnu: r-limma: Update to 3.34.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
2017-12-19gnu: r-edger: Update to 3.20.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
2017-12-19gnu: r-biocstyle: Update to 2.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
2017-12-19gnu: r-dexseq: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
2017-12-19gnu: r-vegan: Update to 2.4-5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
2017-12-18gnu: r-seurat: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0. [propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica, r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr, r-rcppeigen, r-fastica.
2017-12-18gnu: r-seurat: Fix ModularityOptimizer.jar.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class attribute in manifest.
2017-12-15gnu: bedtools: Update to 2.27.1.Ben Woodcroft
* gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
2017-12-14gnu: diamond: Update to 0.9.14.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
2017-12-11gnu: Switch to using the version-major procedure.Christopher Baines
* gnu/packages/audio.scm (ardour)[arguments]: Switch to using version-major. (hmmer)[source]: Switch to using version-major. (pidgin)[native-search-paths]: Switch to using version-major. (r-minimal)[source]: Switch to using version-major.
2017-12-09gnu: bedtools-2.18: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Restore custom install phase. Reported by Mark H Weaver <mhw@netris.org>.
2017-12-06gnu: bedtools: Update to 2.27.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0. [arguments]: Remove custom "install" phase; specify prefix.
2017-12-03gnu: Add kallisto.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kallisto): New variable.
2017-11-30gnu: jellyfish: Update to 2.2.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7. [native-inputs]: Add pkg-config. [inputs]: Add htslib.
2017-11-30gnu: r-annotationhub: Update to 2.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
2017-11-30gnu: r-msnid: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
2017-11-30gnu: r-maldiquant: Update to 1.17.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
2017-11-30gnu: r-genomicalignments: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
2017-11-30gnu: r-limma: Update to 3.34.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
2017-11-30gnu: r-variantannotation: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
2017-11-30gnu: r-getopt: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
2017-11-30gnu: r-gseabase: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
2017-11-30gnu: r-dexseq: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
2017-11-30gnu: r-deseq2: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
2017-11-30gnu: r-annotate: Update to 1.56.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
2017-11-30gnu: metabat: Use scons-build-system.Arun Isaac
* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
2017-11-29gnu: Update r-mutationalpatterns to 1.4.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
2017-11-29gnu: Add r-copynumber.Roel Janssen
* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
2017-11-27gnu: Add java-picard-1.113.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
2017-11-27gnu: Add java-picard.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard): New variable.
2017-11-27gnu: java-htsjdk: Update to 2.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0. [arguments]: Build with JDK 8. [inputs]: Add java-ngs, java-snappy, java-commons-compress, java-commons-logging-minimal, java-commons-jexl-2, and java-xz. [native-inputs]: Add java-testng.
2017-11-27gnu: r-rhdf5: Fix build phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Fix "unpack-smallhdf5" phase.
2017-11-23gnu: subread: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread): Update to 1.6.0.
2017-11-21gnu: idr: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (idr): Update to 2.0.3. [source]: Add snippet to remove generated code.
2017-11-21gnu: idr: Correct license.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (idr)[license]: Change to GPLv2+.
2017-11-18gnu: r-genomeinfodbdata: Update to 0.99.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 0.99.1.
2017-11-18gnu: r-go-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.5.0.
2017-11-18gnu: r-org-ce-eg-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.5.0.
2017-11-18gnu: r-org-dm-eg-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.5.0.
2017-11-18gnu: r-org-mm-eg-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.5.0.
2017-11-18gnu: r-genomationdata: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.
2017-11-18gnu: Remove duplicate from (gnu packages bioinformatics).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
2017-11-18gnu: r-org-hs-eg-db: Clarify description.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.
2017-11-18gnu: r-org-hs-eg-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.5.0.
2017-11-18gnu: r-org-hs-eg-db: Remove duplicate package definition.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Remove duplicate variable.
2017-11-17gnu: Move testing packages from python.scm to check.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-behave-web-api, python2-behave-web-api, python-mock, python2-mock, python-mock-2, python-nose, python2-nose, python-nose2, python2-nose2, python-unittest2, python2-unittest2, python-pytest, python2-pytest, python-pytest-3.0, python2-pytest-3.0, python-pytest-cov, python2-pytest-cov, python-pytest-runner, python2-pytest-runner, python-pytest-mock, python2-pytest-mock, python-pytest-xdist, python2-pytest-xdist, python-scripttest, python2-scripttest, python-testtools, python2-testtools, python-testscenarios, python2-testscenarios, python-testresources, python2-testresources, python-subunit, python2-subunit, python-fixtures, python2-fixtures, python-testrepository, python2-testrepository, python-coverage, python2-coverage, python-cov-core, python2-cov-core, python-testpath, python2-testpath, python-testlib, python2-testlib, python-pytest-cache, python2-pytest-cache, python-pytest-localserver, python-pytest-xprocess, python-pytest-subtesthack, python2-pytest-subtesthack, python-hypothesis, python2-hypothesis, python-lit, python2-lit, python-pytest-pep8, python2-pytest-pep8, python-pytest-flakes, python2-pytest-flakes, python2-coverage-test-runner, python-pylint, python2-pylint, python-paramunittest, python2-python-paramunittest, python-pytest-warnings, python2-pytest-warnings, python-pytest-capturelog, python2-pytest-capturelog, python-pytest-catchlog, python2-pytest-catchlog, python-nosexcover, python2-nosexcover, python-discover, python2-discover, behave, python-rednose, python2-rednose, python-nose-randomly, python2-nose-randomly, python-nose-timer, python2-nose-timer): Move from here... * gnu/packages/check.scm: ...to here. * gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/backup.scm, gnu/packages/bioinformatics.scm, gnu/packages/calendar.scm, gnu/packages/dav.scm, gnu/packages/django.scm, gnu/packages/freedesktop.scm, gnu/packages/haskell.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/ldc.scm, gnu/packages/libffi.scm, gnu/packages/mail.scm, gnu/packages/mpd.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/rdf.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm: Adjust accordingly.
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