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2018-10-21gnu: khmer: Update to 2.1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2. [source]: Fetch from git; remove bundled libraries in snippet. [arguments]: Remove "set-paths" phase; remove "post-install-check" phase; remove "reset-gzip-timestamps" phase. [native-inputs]: Remove seqan and python-nose; add python-cython, python-pytest, and python-pytest-runner. [inputs]: Remove gcc-4.9.
2018-10-21gnu: python-screed: Update to 1.0.Ricardo Wurmus
* 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.
2018-10-21gnu: fasttree: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify install phase.
2018-10-21gnu: express-beta-diversity: Update to 1.0.8.Ricardo Wurmus
* 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.
2018-10-21gnu: edirect: Update to 10.2.20181018.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018. [arguments]: Add simple check phase; simplify other phases. [inputs]: Add perl-xml-simple.
2018-10-21gnu: eigensoft: Update to 7.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1. [arguments]: Remove Makefile modification.
2018-10-21gnu: discrover: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
2018-10-21gnu: Add texlive-latex-examplep.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-examplep): New variable.
2018-10-21gnu: Add texlive-latex-verbatimbox.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-verbatimbox): New variable.
2018-10-21gnu: Add texlive-latex-readarray.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-readarray): New variable.
2018-10-21gnu: Add texlive-generic-listofitems.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-generic-listofitems): New variable.
2018-10-21gnu: Add texlive-latex-doi.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-doi): New variable.
2018-10-21gnu: diamond: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
2018-10-21gnu: delly: Update to 0.7.9.Ricardo Wurmus
* 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.
2018-10-21gnu: deeptools: Update to 3.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
2018-10-21gnu: eolie: Update to 0.9.45.Ricardo Wurmus
* gnu/packages/gnome.scm (eolie): Update to 0.9.45.
2018-10-21gnu: python-dendropy: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
2018-10-21gnu: python-py2bit: Update to 0.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
2018-10-21gnu: cutadapt: Update to 1.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio.
2018-10-21gnu: Add python-dnaio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
2018-10-21gnu: crossmap: Update to 0.2.9.Ricardo Wurmus
* 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.
2018-10-21gnu: python-twobitreader: Update to 3.1.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git.
2018-10-21gnu: Add python-bx-python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python.
2018-10-21gnu: python2-bx-python: Update to 0.8.2.Ricardo Wurmus
* 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.
2018-10-21gnu: bwa-pssm: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
2018-10-21gnu: tophat: Update to 2.1.1.Ricardo Wurmus
* 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.
2018-10-21gnu: linux-libre: Update to 4.18.16.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.16. (%linux-libre-hash): Update hash.
2018-10-21gnu: linux-libre@4.14: Update to 4.14.78.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.78. (%linux-libre-4.14-hash): Update hash.
2018-10-21gnu: linux-libre@4.9: Update to 4.9.135.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135.
2018-10-21gnu: linux-libre@4.4: Update to 4.4.162.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162.
2018-10-21gnu: Add emacs-slime-repl-ansi-color.Pierre Neidhardt
* gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable.
2018-10-21gnu: rng-tools: Update to 6.6.Marius Bakke
* gnu/packages/linux.scm (rng-tools): Update to 6.6.
2018-10-21gnu: fluidsynth: Update to 2.0.1.Marius Bakke
* 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.
2018-10-21gnu: libgxps: Update to 0.3.0.Marius Bakke
* 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.
2018-10-21gnu: libgxps: Propagate required inputs.Marius Bakke
* gnu/packages/gnome.scm (libgxps)[inputs]: Move CAIRO, GLIB and LIBARCHIVE ... [propagated-inputs]: ... here. New field.
2018-10-21gnu: re2: Update to 2018-10-01.Marius Bakke
* gnu/packages/regex.scm (re2): Update to 2018-10-01.
2018-10-21gnu: libgphoto2: Update to 2.5.19.Marius Bakke
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.19.
2018-10-21gnu: appstream-glib: Update to 0.7.14.Marius Bakke
* gnu/packages/glib.scm (appstream-glib): Update to 0.7.14.
2018-10-21gnu: openal: Update to 1.19.1.Marius Bakke
* gnu/packages/audio.scm (openal): Update to 1.19.1.
2018-10-21gnu: kodi: Disable version checker.Efraim Flashner
Fixes bug#32997. * gnu/packages/kodi.scm (kodi)[arguments]: Add substitution to remove the version checking configuration option.
2018-10-21gnu: python2-dendropy: Disable failing test.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable failing test.
2018-10-20gnu: bowtie: Update to 2.3.4.3.Ricardo Wurmus
* 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.
2018-10-20gnu: blast+: Use INVOKE and return #T unconditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and return #T unconditionally.
2018-10-20gnu: bedops: Update to 2.4.35.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35. [source]: Fetch from git.
2018-10-20gnu: bedops: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
2018-10-20gnu: bamm: Fetch from git and use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git. [arguments]: Use INVOKE and return #T unconditionally.
2018-10-20gnu: aragorn: Use invoke and simplify.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build phase; simplify install phase.
2018-10-20gnu: clipper: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1. [source]: Fetch from git. [arguments]: Add fix-typo phase.
2018-10-20gnu: python-pybedtools: Update to 0.7.10.Ricardo Wurmus
* 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.
2018-10-20gnu: Add bedtools-2.26.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
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