| Age | Commit message (Expand) | Author |
|---|
| 2018-10-21 | gnu: python-screed: Update to 1.0....* gnu/packages/bioinformatics.scm (python-screed): Update to 1.0.
[arguments]: Run tests after installation.
[native-inputs]: Add python-pytest, python-pytest-cov, and
python-pytest-runner; remove python-nose.
| Ricardo Wurmus |
| 2018-10-21 | gnu: fasttree: Use INVOKE....* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify
install phase.
| Ricardo Wurmus |
| 2018-10-21 | gnu: express-beta-diversity: Update to 1.0.8....* gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8.
[source]: Fetch from git.
[arguments]: Use INVOKE; remove "exit-source" build phase; simplify.
| Ricardo Wurmus |
| 2018-10-21 | gnu: edirect: Update to 10.2.20181018....* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018.
[arguments]: Add simple check phase; simplify other phases.
[inputs]: Add perl-xml-simple.
| Ricardo Wurmus |
| 2018-10-21 | gnu: eigensoft: Update to 7.2.1....* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1.
[arguments]: Remove Makefile modification.
| Ricardo Wurmus |
| 2018-10-21 | gnu: discrover: Fetch from git....* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add texlive-latex-examplep....* gnu/packages/tex.scm (texlive-latex-examplep): New variable.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add texlive-latex-verbatimbox....* gnu/packages/tex.scm (texlive-latex-verbatimbox): New variable.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add texlive-latex-readarray....* gnu/packages/tex.scm (texlive-latex-readarray): New variable.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add texlive-generic-listofitems....* gnu/packages/tex.scm (texlive-generic-listofitems): New variable.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add texlive-latex-doi....* gnu/packages/tex.scm (texlive-latex-doi): New variable.
| Ricardo Wurmus |
| 2018-10-21 | gnu: diamond: Fetch from git....* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | gnu: delly: Update to 0.7.9....* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9.
[source]: Fetch from git.
[arguments]: Add phase install-templates; use default install phase.
[native-inputs]: Remove python-2.
[home-page]: Use new home page.
* gnu/packages/patches/delly-use-system-libraries.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
| Ricardo Wurmus |
| 2018-10-21 | gnu: deeptools: Update to 3.1.3....* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
| Ricardo Wurmus |
| 2018-10-21 | gnu: eolie: Update to 0.9.45....* gnu/packages/gnome.scm (eolie): Update to 0.9.45.
| Ricardo Wurmus |
| 2018-10-21 | gnu: python-dendropy: Fetch from git....* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | gnu: python-py2bit: Update to 0.3.0....* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
| Ricardo Wurmus |
| 2018-10-21 | gnu: cutadapt: Update to 1.18....* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18.
[inputs]: Add python-dnaio.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add python-dnaio....* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
| Ricardo Wurmus |
| 2018-10-21 | gnu: crossmap: Update to 0.2.9....* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
| Ricardo Wurmus |
| 2018-10-21 | gnu: python-twobitreader: Update to 3.1.6....* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6.
[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | gnu: Add python-bx-python....* gnu/packages/bioinformatics.scm (python-bx-python): New variable.
(python2-bx-python): Define in terms of python-bx-python.
| Ricardo Wurmus |
| 2018-10-21 | gnu: python2-bx-python: Update to 0.8.2....* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2.
[source]: Remove obsolete snippet.
[inputs]: Move python2-numpy from here...
[propagated-inputs]: ...to here; add python2-six.
[native-inputs]: Add python2-lzo and python2-cython.
[home-page]: Update to new home at Github.
| Ricardo Wurmus |
| 2018-10-21 | gnu: bwa-pssm: Fetch from git....* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-21 | gnu: tophat: Update to 2.1.1....* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
| Ricardo Wurmus |
| 2018-10-21 | gnu: linux-libre: Update to 4.18.16....* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.16.
(%linux-libre-hash): Update hash.
| Mark H Weaver |
| 2018-10-21 | gnu: linux-libre@4.14: Update to 4.14.78....* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.78.
(%linux-libre-4.14-hash): Update hash.
| Mark H Weaver |
| 2018-10-21 | gnu: linux-libre@4.9: Update to 4.9.135....* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135.
| Mark H Weaver |
| 2018-10-21 | gnu: linux-libre@4.4: Update to 4.4.162....* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162.
| Mark H Weaver |
| 2018-10-21 | gnu: Add emacs-slime-repl-ansi-color....* gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable.
| Pierre Neidhardt |
| 2018-10-21 | gnu: rng-tools: Update to 6.6....* gnu/packages/linux.scm (rng-tools): Update to 6.6.
| Marius Bakke |
| 2018-10-21 | gnu: fluidsynth: Update to 2.0.1....* gnu/packages/audio.scm (fluidsynth): Update to 2.0.1.
(fluidsynth-1): New public variable.
* gnu/packages/games.scm (gzdoom)[inputs]: Change FLUIDSYNTH to FLUIDSYNTH-1.
* gnu/packages/music.scm (lmms)[inputs]: Likewise.
| Marius Bakke |
| 2018-10-21 | gnu: libgxps: Update to 0.3.0....* gnu/packages/gnome.scm (libgxps): Update to 0.3.0.
[source](patches): Remove.
[build-system]: Switch to MESON-BUILD-SYSTEM.
[inputs]: Change LIBJPEG to LIBJPEG-TURBO.
* gnu/packages/patches/libgxps-CVE-2017-11590.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
| Marius Bakke |
| 2018-10-21 | gnu: libgxps: Propagate required inputs....* gnu/packages/gnome.scm (libgxps)[inputs]: Move CAIRO, GLIB and LIBARCHIVE ...
[propagated-inputs]: ... here. New field.
| Marius Bakke |
| 2018-10-21 | gnu: re2: Update to 2018-10-01....* gnu/packages/regex.scm (re2): Update to 2018-10-01.
| Marius Bakke |
| 2018-10-21 | gnu: libgphoto2: Update to 2.5.19....* gnu/packages/photo.scm (libgphoto2): Update to 2.5.19.
| Marius Bakke |
| 2018-10-21 | gnu: appstream-glib: Update to 0.7.14....* gnu/packages/glib.scm (appstream-glib): Update to 0.7.14.
| Marius Bakke |
| 2018-10-21 | gnu: openal: Update to 1.19.1....* gnu/packages/audio.scm (openal): Update to 1.19.1.
| Marius Bakke |
| 2018-10-21 | gnu: kodi: Disable version checker....Fixes bug#32997.
* gnu/packages/kodi.scm (kodi)[arguments]: Add substitution to remove
the version checking configuration option.
| Efraim Flashner |
| 2018-10-21 | gnu: python2-dendropy: Disable failing test....* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
| Ben Woodcroft |
| 2018-10-20 | gnu: bowtie: Update to 2.3.4.3....* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
| Ricardo Wurmus |
| 2018-10-20 | gnu: blast+: Use INVOKE and return #T unconditionally....* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus |
| 2018-10-20 | gnu: bedops: Update to 2.4.35....* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-10-20 | gnu: bedops: Use INVOKE....* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
| Ricardo Wurmus |
| 2018-10-20 | gnu: bamm: Fetch from git and use INVOKE....* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
| Ricardo Wurmus |
| 2018-10-20 | gnu: aragorn: Use invoke and simplify....* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
| Ricardo Wurmus |
| 2018-10-20 | gnu: clipper: Update to 1.2.1....* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Add fix-typo phase.
| Ricardo Wurmus |
| 2018-10-20 | gnu: python-pybedtools: Update to 0.7.10....* gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10.
[arguments]: Disable broken tests.
[propagated-inputs]: Replace bedtools with bedtools-2.26; add
python-matplotlib, python-pysam, and python-pyyaml.
[native-inputs]: Remove python-pyyaml; add kentutils, python-numpy,
python-pandas, and python-six.
(python-pybedtools): New variable.
| Ricardo Wurmus |
| 2018-10-20 | gnu: Add bedtools-2.26....* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
| Ricardo Wurmus |
| 2018-10-20 | gnu: cataclysm-dda: Update snapshot....* gnu/packages/games.scm (cataclysm-dda): Update snapshot to 0b2c194e5.
| Kei Kebreau |
