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36032 Commits

Author SHA1 Message Date
Ricardo Wurmus 4d93a9a36c
gnu: seqan: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0.
[native-inputs]: Replace bzip2 with xz.
(seqan-1): New variable.
(tophat)[inputs]: Use seqan-1.
 2018-10-21 23:06:47 +02:00
Ricardo Wurmus 4b8f4536ce
gnu: khmer: Update to 2.1.2. 
* 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.
 2018-10-21 23:06:47 +02:00
Ricardo Wurmus 50e33c3a8c
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.
 2018-10-21 23:06:47 +02:00
Ricardo Wurmus 0db75f7a79
gnu: fasttree: Use INVOKE. 
* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify
install phase.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 38622ccd14
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.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus c96ca68f31
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.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 949fa34b84
gnu: eigensoft: Update to 7.2.1. 
* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1.
[arguments]: Remove Makefile modification.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 5748fe5fcc
gnu: discrover: Fetch from git. 
* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 4348a059e5
gnu: Add texlive-latex-examplep. 
* gnu/packages/tex.scm (texlive-latex-examplep): New variable.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus f50f343e0d
gnu: Add texlive-latex-verbatimbox. 
* gnu/packages/tex.scm (texlive-latex-verbatimbox): New variable.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 1d0669f4b4
gnu: Add texlive-latex-readarray. 
* gnu/packages/tex.scm (texlive-latex-readarray): New variable.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 893fbf1285
gnu: Add texlive-generic-listofitems. 
* gnu/packages/tex.scm (texlive-generic-listofitems): New variable.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 49b2e86adf
gnu: Add texlive-latex-doi. 
* gnu/packages/tex.scm (texlive-latex-doi): New variable.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 1c06399358
gnu: diamond: Fetch from git. 
* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 7a1e62ca67
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.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 4d494a4fa3
gnu: deeptools: Update to 3.1.3. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus e6b65bd219
gnu: eolie: Update to 0.9.45. 
* gnu/packages/gnome.scm (eolie): Update to 0.9.45.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 42643fc24d
gnu: python-dendropy: Fetch from git. 
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 6b31040ae6
gnu: python-py2bit: Update to 0.3.0. 
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 6b7260bad1
gnu: cutadapt: Update to 1.18. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18.
[inputs]: Add python-dnaio.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus a5b0038cbd
gnu: Add python-dnaio. 
* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 7321920cd3
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.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 8640f9ec91
gnu: python-twobitreader: Update to 3.1.6. 
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6.
[source]: Fetch from git.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus f5cec0068a
gnu: Add python-bx-python. 
* gnu/packages/bioinformatics.scm (python-bx-python): New variable.
(python2-bx-python): Define in terms of python-bx-python.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 2ba2d62c69
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.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 1d18ee6dfd
gnu: bwa-pssm: Fetch from git. 
* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 9a6808e0c0
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.
 2018-10-21 23:06:45 +02:00
Mark H Weaver f7618bf18e
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.
 2018-10-21 14:59:30 -04:00
Mark H Weaver 668834cae0
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.
 2018-10-21 14:58:03 -04:00
Mark H Weaver c4a7a51292
gnu: linux-libre@4.9: Update to 4.9.135. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135.
 2018-10-21 14:57:24 -04:00
Mark H Weaver 9ab6c680ba
gnu: linux-libre@4.4: Update to 4.4.162. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162.
 2018-10-21 14:56:44 -04:00
Pierre Neidhardt 673364cd3a
gnu: Add emacs-slime-repl-ansi-color. 
* gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable.
 2018-10-21 19:49:10 +02:00
Marius Bakke 3a69b59332
gnu: rng-tools: Update to 6.6. 
* gnu/packages/linux.scm (rng-tools): Update to 6.6.
 2018-10-21 17:57:01 +02:00
Marius Bakke 9b6dc31b6d
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.
 2018-10-21 17:57:01 +02:00
Marius Bakke b6b3e5120a
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.
 2018-10-21 17:57:01 +02:00
Marius Bakke c8d62d936e
gnu: libgxps: Propagate required inputs. 
* gnu/packages/gnome.scm (libgxps)[inputs]: Move CAIRO, GLIB and LIBARCHIVE ...
[propagated-inputs]: ... here.  New field.
 2018-10-21 17:57:01 +02:00
Marius Bakke 920de4286a
gnu: re2: Update to 2018-10-01. 
* gnu/packages/regex.scm (re2): Update to 2018-10-01.
 2018-10-21 17:57:01 +02:00
Marius Bakke ab5e4be647
gnu: libgphoto2: Update to 2.5.19. 
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.19.
 2018-10-21 17:57:01 +02:00
Marius Bakke 8941b4ab3d
gnu: appstream-glib: Update to 0.7.14. 
* gnu/packages/glib.scm (appstream-glib): Update to 0.7.14.
 2018-10-21 17:57:00 +02:00
Marius Bakke 8eadc55202
gnu: openal: Update to 1.19.1. 
* gnu/packages/audio.scm (openal): Update to 1.19.1.
 2018-10-21 17:57:00 +02:00
Efraim Flashner 2c17bd7b29
gnu: kodi: Disable version checker. 
Fixes bug#32997.

* gnu/packages/kodi.scm (kodi)[arguments]: Add substitution to remove
the version checking configuration option.
 2018-10-21 16:39:26 +03:00
Ben Woodcroft 617c478506
gnu: python2-dendropy: Disable failing test. 
* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
 2018-10-21 22:31:56 +10:00
Ricardo Wurmus 21c837405a
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.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus f45093429c
gnu: blast+: Use INVOKE and return #T unconditionally. 
* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus f8b697a385
gnu: bedops: Update to 2.4.35. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus 337d72fb44
gnu: bedops: Use INVOKE. 
* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus c793f4d8fb
gnu: bamm: Fetch from git and use INVOKE. 
* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus 95758e2faf
gnu: aragorn: Use invoke and simplify. 
* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus 8b4102b903
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.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus 895cf8278a
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.
 2018-10-20 23:37:33 +02:00