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2018-11-07gnu: fio: Update to 3.11.Marius Bakke
* gnu/packages/benchmark.scm (fio): Update to 3.11. [source]: Use bz2 compressed tarball.
2018-11-07gnu: kaiju: Update to 1.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07gnu: kaiju: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git. [arguments]: Remove redundant installation step.
2018-11-07gnu: idr: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07gnu: java-htsjdk: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
2018-11-07gnu: hisat2: Use versioned source URL.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07gnu: grit: Update to 2.0.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5. [arguments]: Simplify.
2018-11-07gnu: grit: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07gnu: gemma: Update to 0.98.Ricardo Wurmus
* gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/gemma-intel-compat.patch: Remove file. * gnu/packages/bioinformatics.scm (gemma): Update to 0.98. [source]: Remove patch. [inputs]: Add eigen, gfortran:lib, and openblas. [arguments]: Add phase "find-eigen".
2018-11-07gnu: gemma: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07gnu: clementine: Build with sqlite-with-column-metadata.Pierre Langlois
* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata. Signed-off-by: Leo Famulari <leo@famulari.name>
2018-11-07gnu: fxtract: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07gnu: ribodiff: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07gnu: python-biom-format: Update to 2.1.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7. [arguments]: Add phases "use-cython", "disable-broken-test", and "make-files-writable". [propagated-inputs]: Add python-flake8. [native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
2018-11-07gnu: python-biom-format: Fetch source from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from git.
2018-11-07gnu: bioawk: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07gnu: bedtools-2.18: Fetch sources from stable URL.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release tarball instead of generated tag tarball.
2018-11-07gnu: bamtools: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07gnu: ngless: Install links to required tools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools. [inputs]: Add prodigal, bwa, samtools, and minimap2.
2018-11-07gnu: prodigal: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07services: cuirass: Add 'ttl' configuration field.Ludovic Courtès
* gnu/services/cuirass.scm (<cuirass-configuration>)[ttl]: New field. (cuirass-shepherd-service): Honor it.
2018-11-07gnu: cuirass: Update to 0b40dca.Ludovic Courtès
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
2018-11-07linux-initrd: Make sure 'build-initrd' can delete files.Ludovic Courtès
Fixes <https://bugs.gnu.org/33297>. Reported by Mark H Weaver <mhw@netris.org>. This fixes a regression introduced in 72dc64f8f720268930eed448abfc15d2a0eca3cf, which made files read-only. * gnu/build/linux-initrd.scm (build-initrd): Call 'make-file-writable' on all the files under contents/.
2018-11-07gnu: r-mzr: Update to 2.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0. [inputs]: Remove netcdf. [propagated-inputs]: Add r-ncdf4.
2018-11-07gnu: r-rhdf5lib: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0. [source]: Add snippet to remove bundled binaries. [arguments]: Replace references to hdf5 with references to hdf5-1.10. [native-inputs]: Likewise. [propagated-inputs]: Replace hdf5 with hdf5-1.10.
2018-11-07gnu: r-hdf5array: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
2018-11-07gnu: r-rhdf5: Update to 2.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
2018-11-07gnu: r-rcas: Update to 1.8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0. [native-inputs]: Remove r-testthat and ghc-pandoc-citeproc. [propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges; remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10, r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and r-org-mm-eg-db.
2018-11-07gnu: r-delayedmatrixstats: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0. [propagated-inputs]: Add r-biocparallel and r-hdf5array.
2018-11-07gnu: r-scran: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1. [propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2, r-shiny, and r-viridis.
2018-11-07gnu: r-scater: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0. [propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table, r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
2018-11-07gnu: r-singlecellexperiment: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
2018-11-07gnu: r-beachmat: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0. [propagated-inputs]: Add r-biocgenerics.
2018-11-07gnu: r-qvalue: Update to 2.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
2018-11-07gnu: r-hitc: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
2018-11-07gnu: r-fithic: Update to 1.8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
2018-11-07gnu: r-sushi: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
2018-11-07gnu: r-gwascat: Update to 2.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
2018-11-07gnu: r-gviz: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
2018-11-07gnu: r-gqtlstats: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
2018-11-07gnu: r-ldblock: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
2018-11-07gnu: r-erma: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
2018-11-07gnu: r-snpstats: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
2018-11-07gnu: r-gqtlbase: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
2018-11-07gnu: r-ggbio: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
2018-11-07gnu: r-biovizbase: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
2018-11-07gnu: r-organismdbi: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0. [propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07gnu: r-ensembldb: Update to 2.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.0.
2018-11-07gnu: r-dirichletmultinomial: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.0.
2018-11-07gnu: r-complexheatmap: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.20.0.
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