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2018-11-07gnu: python2-biom-format: Fix build.Ricardo Wurmus
This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa. * gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify phases of base package.
2018-11-07gnu: raxml: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
2018-11-07gnu: pyicoteo: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
2018-11-07gnu: hplip: Remove bundled non-free blobs.Efraim Flashner
This fixes <https://bugs.gnu.org/32184>. * gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to remove non-free code and binary blobs. * gnu/packages/patches/hplip-remove-imageprocessor.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2018-11-07gnu: sra-tools: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
2018-11-07gnu: libgff: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07gnu: kentutils: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git. [arguments]: Add phase "fix-permissions".
2018-11-07gnu: r-seqgl: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
2018-11-07gnu: pplacer: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git. [arguments]: Make files writable; use INVOKE.
2018-11-07gnu: minced: Update to 0.3.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
2018-11-07gnu: minced: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07gnu: metabat: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07gnu: mash: Update to 2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07gnu: mash: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
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.
2018-11-07gnu: cuirass: Update to 0b40dca.Ludovic Courtès
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
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.
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