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* Merge branch 'master' into core-updatesLeo Famulari2017-12-21
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| * gnu: r-biomart: Update to 2.34.1.Ricardo Wurmus2017-12-19
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1. [propagated-inputs]: Add r-httr.
| * gnu: r-gviz: Update to 1.22.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
| * gnu: r-gqtlstats: Update to 1.10.1.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
| * gnu: r-rtracklayer: Update to 1.38.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
| * gnu: r-limma: Update to 3.34.4.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
| * gnu: r-edger: Update to 3.20.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
| * gnu: r-biocstyle: Update to 2.6.1.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
| * gnu: r-dexseq: Update to 1.24.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
| * gnu: r-vegan: Update to 2.4-5.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
* | gnu: Remove redundant cmake libdir configure flags.Efraim Flashner2017-12-19
|/ | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (imp)[arguments]: Remove CMAKE_INSTALL_LIBDIR flag. * gnu/packages/calendar.scm (libical): Same. * gnu/packages/engineering.scm (kicad): Same. * gnu/packages/games.scm (openrct2, mgba): Same. * gnu/packages/gl.scm (virtualgl): Same. * gnu/packages/image-processing.scm (mia): Same. * gnu/packages/linux.scm (rdma-core): Same. * gnu/packages/machine-learning.scm (dlib): Same. * gnu/packages/maths.scm (lapack, superlu, z3): Same. * gnu/packages/password-utils.scm (keepassxc): Same. * gnu/packages/photo.scm (darktable): Same. * gnu/packages/rdesktop.scm (freerdp): Same.
* gnu: r-seurat: Update to 2.1.0.Ricardo Wurmus2017-12-18
| | | | | | | * 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.
* gnu: r-seurat: Fix ModularityOptimizer.jar.Ricardo Wurmus2017-12-18
| | | | | * gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class attribute in manifest.
* gnu: bedtools: Update to 2.27.1.Ben Woodcroft2017-12-15
| | | | * gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
* gnu: diamond: Update to 0.9.14.Ben Woodcroft2017-12-14
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
* gnu: Switch to using the version-major procedure.Christopher Baines2017-12-11
| | | | | | | * 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.
* gnu: bedtools-2.18: Fix build.Ricardo Wurmus2017-12-09
| | | | | | | * gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Restore custom install phase. Reported by Mark H Weaver <mhw@netris.org>.
* gnu: bedtools: Update to 2.27.0.Ricardo Wurmus2017-12-06
| | | | | * gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0. [arguments]: Remove custom "install" phase; specify prefix.
* gnu: Add kallisto.Ricardo Wurmus2017-12-03
| | | | * gnu/packages/bioinformatics.scm (kallisto): New variable.
* gnu: jellyfish: Update to 2.2.7.Ricardo Wurmus2017-11-30
| | | | | | * gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7. [native-inputs]: Add pkg-config. [inputs]: Add htslib.
* gnu: r-annotationhub: Update to 2.10.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
* gnu: r-msnid: Update to 1.12.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
* gnu: r-maldiquant: Update to 1.17.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
* gnu: r-genomicalignments: Update to 1.14.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
* gnu: r-limma: Update to 3.34.2.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
* gnu: r-variantannotation: Update to 1.24.2.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
* gnu: r-getopt: Update to 1.20.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
* gnu: r-gseabase: Update to 1.40.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
* gnu: r-dexseq: Update to 1.24.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
* gnu: r-deseq2: Update to 1.18.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
* gnu: r-annotate: Update to 1.56.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
* gnu: metabat: Use scons-build-system.Arun Isaac2017-11-30
| | | | * gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
* gnu: Update r-mutationalpatterns to 1.4.1.Roel Janssen2017-11-29
| | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
* gnu: Add r-copynumber.Roel Janssen2017-11-29
| | | | * gnu/packages/bioinformatics.scm (r-copynumber): New variable.
* gnu: Add java-picard-1.113.Ricardo Wurmus2017-11-27
| | | | * gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
* gnu: Add java-picard.Ricardo Wurmus2017-11-27
| | | | * gnu/packages/bioinformatics.scm (java-picard): New variable.
* gnu: java-htsjdk: Update to 2.3.0.Ricardo Wurmus2017-11-27
| | | | | | | | * 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.
* gnu: r-rhdf5: Fix build phase.Ricardo Wurmus2017-11-27
| | | | | * gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Fix "unpack-smallhdf5" phase.
* gnu: subread: Update to 1.6.0.Ricardo Wurmus2017-11-23
| | | | * gnu/packages/bioinformatics.scm (subread): Update to 1.6.0.
* gnu: idr: Update to 2.0.3.Ricardo Wurmus2017-11-21
| | | | | * gnu/packages/bioinformatics.scm (idr): Update to 2.0.3. [source]: Add snippet to remove generated code.
* gnu: idr: Correct license.Ricardo Wurmus2017-11-21
| | | | * gnu/packages/bioinformatics.scm (idr)[license]: Change to GPLv2+.
* gnu: r-genomeinfodbdata: Update to 0.99.1.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 0.99.1.
* gnu: r-go-db: Update to 3.5.0.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-go-db): Update to 3.5.0.
* gnu: r-org-ce-eg-db: Update to 3.5.0.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.5.0.
* gnu: r-org-dm-eg-db: Update to 3.5.0.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.5.0.
* gnu: r-org-mm-eg-db: Update to 3.5.0.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.5.0.
* gnu: r-genomationdata: Update to 1.10.0.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.
* gnu: Remove duplicate from (gnu packages bioinformatics).Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
* gnu: r-org-hs-eg-db: Clarify description.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.
* gnu: r-org-hs-eg-db: Update to 3.5.0.Ricardo Wurmus2017-11-18
| | | | * gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.5.0.
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