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2018-11-07gnu: ritornello: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1. [arguments]: Adjust file patching.
2018-11-07gnu: ritornello: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07gnu: snap-aligner: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git. [arguments]: Use INVOKE.
2018-11-07gnu: sortmerna: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07gnu: vsearch: Fetch source from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07gnu: preseq: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
2018-11-07gnu: preseq: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07gnu: seqtk: Update to 1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3. [source]: Remove outdated snippet. [arguments]: Use INVOKE and return #T unconditionally.
2018-11-07gnu: seqtk: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07gnu: raxml: Update to 8.2.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
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.
2018-11-07pull: Add missing monadic 'return'.Ludovic Courtès
Fixes a regression introduced in 5f7dd092ca577a534067f577b8849ed06cabf970 where, upon completion, 'guix pull' would fail (instead of printing the new/upgraded packages) with ugly errors like: successfully built /gnu/store/…-profile.drv 1 package in profile Backtrace: […] In guix/store.scm: 1605:24 1 (run-with-store _ _ #:guile-for-build _ #:system _ # _) In unknown file: 0 (_ #<build-daemon 256.97 2476b40>) ERROR: Wrong type to apply: #t Reported by thorwil on #guix. * guix/scripts/pull.scm (build-and-install): Add missing 'return' when DRY-RUN? is wrong.
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.
2018-11-07services: 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.
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