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36103 Commits

Author SHA1 Message Date
Marius Bakke e810de3e68
gnu: python-m2crypto: python-typing is only needed for python2. 
* gnu/packages/python-crypto.scm (python-m2crypto)[propagated-inputs]: Remove.
[properties]: New field.
(python2-m2crypto)[propagated-inputs]: Add PYTHON2-TYPING.
 2018-10-22 23:01:19 +02:00
Marius Bakke 90fb136ff7
gnu: xorg-server: Update to 1.20.2. 
* gnu/packages/xorg.scm (xorg-server): Update to 1.20.2.
 2018-10-22 23:01:19 +02:00
Marius Bakke 4350cacdf7
gnu: xf86-input-libinput: Update to 0.28.1. 
* gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.28.1.
 2018-10-22 23:01:18 +02:00
Marius Bakke 3743e117a6
gnu: libmd: Update to 1.0.1. 
* gnu/packages/crypto.scm (libmd): Update to 1.0.1.
 2018-10-22 23:01:18 +02:00
Marius Bakke f38eedd518
gnu: samba: Update to 4.8.6. 
* gnu/packages/samba.scm (samba): Update to 4.8.6.
 2018-10-22 23:01:18 +02:00
Marius Bakke 3ad0a35890
gnu: Add GN. 
* gnu/packages/build-tools.scm (gn): New public variable.
 2018-10-22 23:01:18 +02:00
Marius Bakke f232c875d2
gnu: python-lazy-object-proxy: Update to 1.3.1. 
* gnu/packages/python.scm (python-lazy-object-proxy): Update to 1.3.1.
 2018-10-22 23:01:18 +02:00
Marius Bakke b45688313b
gnu: python-mistune: Update to 0.8.4. 
* gnu/packages/python.scm (python-mistune): Update to 0.8.4.
 2018-10-22 23:01:18 +02:00
Meiyo Peng 9861bcd182
gnu: liblxqt: Update to 0.13.0. 
* gnu/packages/lxqt.scm (liblxqt): Update to 0.13.0.
[source]: Remove patches.
[home-page]: Use HTTPS.
* gnu/packages/patches/liblxqt-include.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-10-22 22:09:51 +08:00
Meiyo Peng 50401c2a68
gnu: libqtxdg: Update to 3.2.0. 
* gnu/packages/lxqt.scm (libqtxdg): Update to 3.2.0.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-10-22 22:09:51 +08:00
Christopher Lemmer Webber 51f4e36cb9
gnu: Add emacs-scribble-mode. 
* gnu/packages/emacs.scm (emacs-scribble-mode): New variable.
 2018-10-22 09:59:42 -04:00
Nicolas Goaziou 3a352a4405
gnu: snap: Update to 4.2.2.2. 
* gnu/packages/education.scm (snap): Update to 4.2.2.2.  Update source URL.
 2018-10-22 15:56:38 +02:00
Ricardo Wurmus 09aa3d063a
gnu: Add r-ruvseq. 
* gnu/packages/bioconductor.scm (r-ruvseq): New variable.
 2018-10-22 13:00:24 +02:00
Leo Famulari 318ec0a896
gnu: livemedia-utils: Update to 2018.10.17 [fixes CVE-2018-4013]. 
* gnu/packages/video.scm (livemedia-utils): Update to 2018.10.17.
 2018-10-22 03:37:53 -04:00
Leo Famulari 69c69c2d8e
gnu: libmpdclient: Update to 2.16. 
* gnu/packages/mpd.scm (libmpdclient): Update to 2.16.
 2018-10-21 23:55:28 -04:00
Tobias Geerinckx-Rice dc3dfa131f
gnu: knot: Update to 2.7.3. 
* gnu/packages/dns.scm (knot): Update to 2.7.3.
 2018-10-22 00:40:05 +02:00
Leo Famulari df71447e99
gnu: OpenSSH: Update to 7.9p1. 
* gnu/packages/ssh.scm (openssh): Update to 7.9p1.
 2018-10-21 18:33:58 -04:00
Pierre Langlois ff598353c0
gnu: light: Update to 1.2. 
* gnu/packages/linux.scm (light): Update to 1.2.
[source]: Switch to url-fetch.
[arguments]: Remove.
[native-inputs]: Remove help2man. Add autoconf and automake.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-10-21 23:54:46 +02:00
Luther Thompson 16d212510a
gnu: Add python-ilinkedlist. 
* gnu/packages/python.scm (python-ilinkedlist): New variable.
 2018-10-21 23:54:46 +02:00
Ludovic Courtès aff38cb199
install: Make /var/guix/…/guix-profile a relative symlink. 
* gnu/build/install.scm (populate-single-profile-directory): Make
/var/guix/profiles/per-user/root/guix-profile a relative symlink.
 2018-10-21 23:54:46 +02:00
Ricardo Wurmus f8ee22fc8b
gnu: flexbar: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0.
[source]: Fetch from git.
[arguments]: Adjust check and install phases.
[home-page]: Update to new home at Github.
[license]: Change to bsd-3.
 2018-10-21 23:06:47 +02:00
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