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Author SHA1 Message Date
Ben J Woodcroft
67f66812f5
gnu: Add python-termcolor. 
* gnu/packages/python.scm (python-termcolor, python2-termcolor): New
variables.
 2016-09-27 20:07:02 +10:00
Marius Bakke
f536dce522
gnu: python-pysam: Enable tests. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
 2016-09-27 20:06:00 +10:00
Marius Bakke
dff26b2363
gnu: python-pysam: Delete bundled htslib. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
 2016-09-27 20:06:00 +10:00
Marius Bakke
397d463a12
gnu: python-pysam: Use 'modify-phases'. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.
 2016-09-27 20:06:00 +10:00
Marius Bakke
bdc7be59eb
gnu: Add bcftools. 
* gnu/packages/bioinformatics.scm (bcftools): New variable.
 2016-09-27 20:06:00 +10:00
Marius Bakke
e301bfc886
gnu: python2-pbcore: Update to 1.2.10. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.
 2016-09-27 20:06:00 +10:00
Marius Bakke
c2efe1aea8
gnu: Add python-pyxb. 
* gnu/packages/xml.scm (python-pyxb, python2-pyxb): New variables.
 2016-09-27 20:06:00 +10:00
Marius Bakke
fd49eb213f
gnu: python-pysam: Update to 0.9.1.4. 
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.
 2016-09-27 20:05:57 +10:00
Ludovic Courtès
8a54c0ec69
guix build: Gracefully handle packages without source for '-S'. 
Fixes <http://bugs.gnu.org/22836>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/scripts/build.scm (options->derivations): Gracefully
handle (package-source p) = #f.
 2016-09-27 11:44:56 +02:00
Ludovic Courtès
3c185b24f5
Add missing exports. 
Reported by Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
at <https://lists.gnu.org/archive/html/guix-devel/2016-09/msg01686.html>.

* gnu/system/file-systems.scm (%tty-gid): Export.
* guix/build-system/python.scm (default-python, default-python2):
Export.
 2016-09-27 11:22:56 +02:00
Leo Famulari
9ad0965228
gnu: openssl-next: Update to 1.1.0b [fixes CVE-2016-6309]. 
* gnu/packages/tls.scm (openssl-next): Update to 1.1.0b.
 2016-09-26 17:09:08 -04:00
Leo Famulari
8be42e5daf
gnu: openssl: Update replacement to 1.0.2j [fixes CVE-2016-7052]. 
* gnu/packages/tls.scm (openssl): Update replacement to 1.0.2j.
(openssl-1.0.2i): Replace with...
(openssl-1.0.2j): ... new variable.
 2016-09-26 17:09:05 -04:00
Danny Milosavljevic
58478cc1cb
gnu: libftdi: Propagate the libusb input. 
* gnu/packages/libftdi.scm (libftdi): Change libusb from an input to a
propagated-input.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-26 14:30:37 -04:00
Ricardo Wurmus
675d7ae26f
gnu: ncbi-vdb: Only build on i686 and x86_64. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.
 2016-09-26 14:30:59 +02:00
Ricardo Wurmus
bc600b80a2
gnu: ghc-pandoc: Update to 1.17.2. 
* gnu/packages/haskell.scm (ghc-pandoc): Update to 1.17.2.
 2016-09-26 14:30:59 +02:00
Ricardo Wurmus
5a502d9abd
gnu: ghc-texmath: Update to 0.8.6.5. 
* gnu/packages/haskell.scm (ghc-texmath): Update to 0.8.6.5.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
2e9b1276b7
gnu: ghc-cmark: Update to 0.5.3.1. 
* gnu/packages/haskell.scm (ghc-cmark): Update to 0.5.3.1.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
8f1e2dca55
gnu: ghc-highlighting-kate: Update to 0.6.3. 
* gnu/packages/haskell.scm (ghc-highlighting-kate): Update to 0.6.3.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
ae87e4fcde
gnu: ghc-pandoc-types: Update to 1.16.1.1. 
* gnu/packages/haskell.scm (ghc-pandoc-types): Update to 1.16.1.1.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
1da48e4302
gnu: ghc-tagsoup: Update to 0.14. 
* gnu/packages/haskell.scm (ghc-tagsoup): Update to 0.14.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
1a545a1e7c
gnu: tbb: Fail on test errors. 
* gnu/packages/tbb.scm (tbb)[arguments]: Add phase
"fail-on-test-errors".
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
ba4529c4f7
gnu: ghc-tls: Update to 1.3.8. 
* gnu/packages/haskell.scm (ghc-tls): Update to 1.3.8.
 2016-09-26 14:30:57 +02:00
Ricardo Wurmus
7f5ca399bf
gnu: tbb: Use modify-phases syntax. 
* gnu/packages/tbb.scm (tbb)[arguments]: Use "modify-phases" syntax.
 2016-09-26 14:30:57 +02:00
Ben Woodcroft
af8de20386
gnu: vsearch: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
 2016-09-26 20:35:32 +10:00
Ricardo Wurmus
204adc3017
gnu: azr3: Fix libsigc++ build errors. 
* gnu/packages/audio.scm (azr3)[arguments]: Add "-std=gnu++11" flag.
[source]: Add patch.
* gnu/packages/patches/azr3.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-09-26 10:47:58 +02:00
Ricardo Wurmus
3ef08dceb3
gnu: qtractor: Update to 0.7.9. 
* gnu/packages/music.scm (qtractor): Update to 0.7.9.
 2016-09-26 08:16:13 +02:00
Ricardo Wurmus
7ddc178093
profiles: Build GTK+ input module cache. 
* guix/profiles.scm (gtk-im-modules): New procedure.
(%default-profile-hooks): Add it.
 2016-09-26 07:58:17 +02:00
Ricardo Wurmus
2c9f4786c9
profiles: manifest-lookup-package: Optionally match version prefix. 
* guix/profiles.scm (manifest-lookup-package): Optionally filter store
item matches by version prefix.
 2016-09-26 07:58:17 +02:00
Ricardo Wurmus
f3cfe4515a
gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene. 
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
  New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
684f29bd2e
gnu: Add r-grohmm. 
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
7f903d7300
gnu: Add r-systempiper. 
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
cb99d457f0
gnu: Add r-shortread. 
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
89f40c5e4e
gnu: Add r-gostats. 
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
1a1931f7e0
gnu: Add r-category. 
* gnu/packages/bioinformatics.scm (r-category): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
ad740ff818
gnu: Add r-gseabase. 
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
 2016-09-26 07:47:53 +02:00
Ricardo Wurmus
cd9e7dc7ff
gnu: Add r-rbgl. 
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
 2016-09-26 03:25:23 +02:00
Ricardo Wurmus
e816377374
gnu: Add r-annotationforge. 
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
 2016-09-26 03:25:17 +02:00
Ricardo Wurmus
9e330278ee
gnu: Add r-batchjobs. 
* gnu/packages/statistics.scm (r-batchjobs): New variable.
 2016-09-26 03:25:11 +02:00
Ricardo Wurmus
dc4fb16d25
gnu: Add r-fail. 
* gnu/packages/statistics.scm (r-fail): New variable.
 2016-09-26 03:25:06 +02:00
Ricardo Wurmus
cd26ec3bbf
gnu: Add r-bbmisc. 
* gnu/packages/statistics.scm (r-bbmisc): New variable.
 2016-09-26 03:25:02 +02:00
Ricardo Wurmus
929d4aaea1
gnu: Add r-checkmate. 
* gnu/packages/statistics.scm (r-checkmate): New variable.
 2016-09-26 03:24:59 +02:00
Ricardo Wurmus
0d90462fa3
gnu: Add r-backports. 
* gnu/packages/statistics.scm (r-backports): New variable.
 2016-09-26 03:24:55 +02:00
Ricardo Wurmus
8e1bfc7e8c
gnu: Add r-sendmailr. 
* gnu/packages/statistics.scm (r-sendmailr): New variable.
 2016-09-26 03:24:50 +02:00
Ricardo Wurmus
0c77fd50f8
gnu: Add r-pheatmap. 
* gnu/packages/statistics.scm (r-pheatmap): New variable.
 2016-09-26 03:24:44 +02:00
Ricardo Wurmus
092197a548
gnu: Add r-matrix. 
* gnu/packages/statistics.scm (r-matrix): New variable.
 2016-09-26 03:21:32 +02:00
Ricardo Wurmus
ad34f0ac96
gnu: Add r-deseq2. 
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
 2016-09-26 03:21:27 +02:00
Ricardo Wurmus
2301fd3e4d
gnu: Add r-genefilter. 
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
 2016-09-26 03:21:19 +02:00
Ricardo Wurmus
2d21d44dbd
gnu: Add r-hmisc. 
* gnu/packages/statistics.scm (r-hmisc): New variable.
 2016-09-26 03:21:13 +02:00
Ricardo Wurmus
07a664cde0
gnu: Add r-geneplotter. 
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
 2016-09-26 03:21:07 +02:00
Ricardo Wurmus
8c6de58849
gnu: Add r-annotate. 
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
 2016-09-26 03:20:59 +02:00