| Age | Commit message (Expand) | Author |
|---|
| 2018-11-07 | gnu: Add spread-sheet-widget.•••* gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
| Kei Kebreau |
| 2018-11-07 | gnu: filevercmp: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ritornello: Update to 2.0.1.•••* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ritornello: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: snap-aligner: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
| Ricardo Wurmus |
| 2018-11-07 | gnu: sortmerna: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: vsearch: Fetch source from git.•••* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: preseq: Update to 2.0.3.•••* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
| Ricardo Wurmus |
| 2018-11-07 | gnu: preseq: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: seqtk: Update to 1.3.•••* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
| Ricardo Wurmus |
| 2018-11-07 | gnu: seqtk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: raxml: Update to 8.2.12.•••* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python2-biom-format: Fix build.•••This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa.
* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
| Ricardo Wurmus |
| 2018-11-07 | gnu: raxml: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: pyicoteo: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: hplip: Remove bundled non-free blobs.•••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.
| Efraim Flashner |
| 2018-11-07 | gnu: sra-tools: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: libgff: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: kentutils: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-seqgl: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: pplacer: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
| Ricardo Wurmus |
| 2018-11-07 | gnu: minced: Update to 0.3.2.•••* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
| Ricardo Wurmus |
| 2018-11-07 | gnu: minced: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: metabat: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: mash: Update to 2.1.•••* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
| Ricardo Wurmus |
| 2018-11-07 | gnu: mash: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: fio: Update to 3.11.•••* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
| Marius Bakke |
| 2018-11-07 | gnu: kaiju: Update to 1.6.3.•••* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
| Ricardo Wurmus |
| 2018-11-07 | gnu: kaiju: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
| Ricardo Wurmus |
| 2018-11-07 | gnu: idr: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: java-htsjdk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: hisat2: Use versioned source URL.•••* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
| Ricardo Wurmus |
| 2018-11-07 | gnu: grit: Update to 2.0.5.•••* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
| Ricardo Wurmus |
| 2018-11-07 | gnu: grit: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: gemma: Update to 0.98.•••* 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".
| Ricardo Wurmus |
| 2018-11-07 | gnu: gemma: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: clementine: Build with sqlite-with-column-metadata.•••* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata.
Signed-off-by: Leo Famulari <leo@famulari.name>
| Pierre Langlois |
| 2018-11-07 | gnu: fxtract: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ribodiff: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python-biom-format: Update to 2.1.7.•••* 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.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python-biom-format: Fetch source from git.•••* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bioawk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bedtools-2.18: Fetch sources from stable URL.•••* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bamtools: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ngless: Install links to required tools.•••* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
| Ricardo Wurmus |
| 2018-11-07 | gnu: prodigal: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | services: cuirass: Add 'ttl' configuration field.•••* gnu/services/cuirass.scm (<cuirass-configuration>)[ttl]: New field.
(cuirass-shepherd-service): Honor it.
| Ludovic Courtès |
| 2018-11-07 | gnu: cuirass: Update to 0b40dca.•••* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
| Ludovic Courtès |
| 2018-11-07 | linux-initrd: Make sure 'build-initrd' can delete files.•••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/.
| Ludovic Courtès |
| 2018-11-07 | gnu: r-mzr: Update to 2.16.0.•••* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
| Ricardo Wurmus |
