ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-12-28 07:12:30 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions
13038 commits 1 branch 0 tags 448 MiB
Commit graph

297 commits

Author SHA1 Message Date
Roel Janssen
a0a71439fa gnu: Add bioawk. 
* gnu/packages/bioinformatics.scm (bioawk): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-03-10 18:37:25 -05:00
Ricardo Wurmus
649e9b3b47 gnu: python-pysam: Move cython and setuptools to native inputs. 
* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move
"python-cython" and "python-setuptools" from here...
[native-inputs]: ... to here.
 2016-03-03 13:47:19 +01:00
Ricardo Wurmus
3acb8c857c gnu: deeptools: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
 2016-03-03 13:47:12 +01:00
Ricardo Wurmus
14bda1ff49 gnu: deeptools: Change "propagated-inputs" to "inputs". 
* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
 2016-03-03 13:47:02 +01:00
Ricardo Wurmus
69e0e03c36 gnu: Add python-pybigwig. 
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
  New variables.
 2016-03-03 13:46:52 +01:00
Ricardo Wurmus
d454640c38 gnu: python-pysam: Update to 0.8.4. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
 2016-03-03 13:46:39 +01:00
Ricardo Wurmus
55a9a8c2b9 gnu: python-pysam, python2-pysam: Move to bioinformatics.scm. 
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
  ...here.
 2016-03-03 13:46:26 +01:00
Pjotr Prins
f82c8c3cba gnu: r-go-db: Bioconductor changed URL for data downloads. 
* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
 2016-03-01 19:47:26 +02:00
Pjotr Prins
27acfaea4c gnu: r-iranges: Update to 2.4.8. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
 2016-03-01 19:47:26 +02:00
Pjotr Prins
8921841da8 gnu: r-s4vectors: Update to 0.8.11. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
 2016-03-01 19:47:25 +02:00
Ricardo Wurmus
d1e32822b4 gnu: Add PePr. 
* gnu/packages/bioinformatics.scm (pepr): New variable.
 2016-03-01 11:51:24 +01:00
Ricardo Wurmus
d29150b55d gnu: Add bwa-pssm. 
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
 2016-03-01 10:31:04 +01:00
Mark H Weaver
b35461748b gnu: Fix misplaced commas (unquote). 
Fix many occurrences of comma (unquote) being placed immediately after the
previous list item, e.g. ("ncurses", ncurses) in the inputs.

* gnu/packages/base.scm (patch, gnu-make),
  gnu/packages/bioinformatics.scm (hmmer),
  gnu/packages/bittorrent.scm (aria2),
  gnu/packages/compression.scm (pbzip2),
  gnu/packages/databases.scm (recutils),
  gnu/packages/fonts.scm (font-terminus),
  gnu/packages/freedesktop.scm (xdg-utils, elogind),
  gnu/packages/games.scm (gnujump),
  gnu/packages/gnome.scm (libidl, gnumeric, eog, gedit),
  gnu/packages/gnunet.scm (gnunet),
  gnu/packages/gnuzilla.scm (mozjs, nspr),
  gnu/packages/gtk.scm (gtksourceview, gdk-pixbuf),
  gnu/packages/lua.scm (lua),
  gnu/packages/openstack.scm (python-swiftclient),
  gnu/packages/perl.scm (perl-json-any),
  gnu/packages/polkit.scm (polkit-qt),
  gnu/packages/python.scm (wrap-python3, python-oauthlib)
  (python-mccabe-0.2.1, python-contextlib2, python2-rauth),
  gnu/packages/qt.scm (qtkeychain),
  gnu/packages/ruby.scm (ruby-nokogiri),
  gnu/packages/screen.scm (screen),
  gnu/packages/ssh.scm (libssh),
  gnu/packages/video.scm (ffmpeg, mplayer),
  gnu/packages/vim.scm (vim),
  gnu/packages/xdisorg.scm (redshift),
  gnu/packages/xfce.scm (xfce4-panel, xfce4-settings),
  gnu/packages/xnee.scm (xnee),
  gnu/packages/xorg.scm (font-adobe100dpi, font-adobe75dpi),
  gnu/packages/zsh.scm (zsh): Fix misplaced commas (unquote).
 2016-02-27 08:49:26 -05:00
Ludovic Courtès
736f9ffce2 gnu: Add missing import in bioinformatics.scm. 
This is a followup to 1baee94.

* gnu/packages/bioinformatics.scm: Add missing import.
 2016-02-25 12:48:08 +01:00
Ricardo Wurmus
1baee943ca gnu: Add libBigWig. 
* gnu/packages/bioinformatics.scm (libbigwig): New variable.
 2016-02-25 11:43:44 +01:00
Ricardo Wurmus
6d415db23d gnu: r-topgo: Add missing input. 
* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add
  "r-graph".
 2016-02-24 17:36:55 +01:00
Ricardo Wurmus
d1dbde6ac1 gnu: Add r-graph. 
* gnu/packages/bioinformatics.scm (r-graph): New variable.
 2016-02-24 17:36:55 +01:00
Ricardo Wurmus
e761beb9a9 gnu: Add r-org-mm-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Ricardo Wurmus
16c53a1e26 gnu: Add r-org-dm-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Ricardo Wurmus
fefedf98cb gnu: Add r-org-ce-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Ricardo Wurmus
486da49143 gnu: Add r-org-hs-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Ricardo Wurmus
578b05d99e gnu: htseq: Add PySam to inputs. 
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".
 2016-02-16 15:32:15 +01:00
Ricardo Wurmus
d15d981ea2 gnu: Add StringTie. 
* gnu/packages/bioinformatics.scm (stringtie): New variable.
 2016-02-16 14:51:10 +01:00
Ben Woodcroft
e70f7a2306 gnu: prodigal: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
 2016-02-16 07:18:59 +10:00
Ricardo Wurmus
258c0a365e gnu: r-annotationdbi: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
 2016-02-15 16:11:22 +01:00
Ben Woodcroft
cf6edaba74 gnu: vsearch: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0.
[origin]: Adapt to changes in bundling of cityhash.
 2016-02-15 22:54:25 +10:00
Ricardo Wurmus
0d0bcaa08e gnu: macs: Update to 2.1.0.20151222. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
 2016-02-12 18:16:16 +01:00
Ricardo Wurmus
43ec07f17c gnu: macs: Use "pypi-uri". 
* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to
  build source URI.
 2016-02-12 18:16:16 +01:00
Ben J. Woodcroft
ce294c0445 gnu: Update sortmerna to 2.1. 
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
 2016-02-02 22:42:38 +10:00
Ben Woodcroft
a78d62f432 gnu: sra-tools: Update to 2.5.7. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
 2016-01-26 10:59:13 +10:00
Ben Woodcroft
fe91666b79 gnu: ncbi-vdb: Update to 2.5.7. 
gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
 2016-01-26 10:59:13 +10:00
Ben Woodcroft
d3b39bc231 gnu: ngs-sdk: Update to 1.2.3. 
gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
 2016-01-26 10:59:13 +10:00
Ben Woodcroft
bcadaf0050 gnu: Add sortmerna. 
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
 2016-01-25 08:35:11 +10:00
Ricardo Wurmus
3a40a92c73 gnu: Add cufflinks. 
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
 2016-01-23 09:15:11 +01:00
Ricardo Wurmus
94ce537eac gnu: Add TopHat. 
* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-23 08:53:10 +01:00
Ricardo Wurmus
3062d750b4 gnu: star: Update to 2.5.1b. 
* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
 2016-01-23 08:40:14 +01:00
Ricardo Wurmus
c0266e8d03 gnu: star: Use "modify-phases" syntax. 
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
  syntax.
 2016-01-23 08:40:14 +01:00
Pjotr Prins
897092875e gnu: r-qtl: Update to 1.38-4. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
 2016-01-21 11:16:12 +01:00
Ricardo Wurmus
2309ed6862 gnu: samtools-0.1: Adapt to changes in "samtools" variable. 
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
  "LIBCURSES" make flag; delete "configure" phase; disable tests outside
  of "substitute-keyword-arguments".
 2016-01-16 15:50:51 +01:00
Ricardo Wurmus
3141b83d4d gnu: r-go-db: Add missing input. 
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
  "r-annotationdbi".
 2016-01-14 14:43:59 +01:00
Ricardo Wurmus
0047d26a22 gnu: bowtie: Update to 2.2.6. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
 2016-01-14 14:43:25 +01:00
Ben Woodcroft
6b6f7d6a0e gnu: orfm: Update to 0.5.3. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
 2016-01-14 08:00:10 +10:00
Ricardo Wurmus
c44734115a gnu: samtools: Update to 1.3. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
 2016-01-13 15:12:22 +01:00
Ben Woodcroft
81f3e0c1f3 gnu: Add fxtract. 
* gnu/packages/bioinformatics.scm (fxtract): New variable.
 2016-01-12 07:49:19 +10:00
Ben Woodcroft
9b9b7ffd8e gnu: bedtools: Update to 2.25.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'.  Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
 2016-01-11 00:36:13 +10:00
Ben Woodcroft
6573ac82ad gnu: bedtools: Use modify-phases. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
 2016-01-11 00:36:13 +10:00
Mathieu Lirzin
2409f37f28 gnu: Add missing (gnu packages gcc) import. 
* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
 2016-01-08 14:18:46 +01:00
Ricardo Wurmus
cb933df6da gnu: Add genomation. 
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
03ea5a357e gnu: Add seqPattern. 
* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
c43a011de3 gnu: Add impute. 
* gnu/packages/bioinformatics.scm (r-impute): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
c63cef6699 gnu: Add BSgenome. 
* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
d547ce5e70 gnu: Add topGO. 
* gnu/packages/bioinformatics.scm (r-topgo): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
fb25d8803f gnu: Add GO.db. 
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
2fd7c04984 gnu: Add GenomicFeatures. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
317755ff0f gnu: Add rtracklayer. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
d8a828af78 gnu: Add GenomicAlignments. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
6e76dda2d0 gnu: Add SummarizedExperiment. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
f8d74f7018 gnu: Add Rsamtools. 
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
bf15935337 gnu: Add Biostrings. 
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
e91d362e48 gnu: Add BiocParallel. 
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
c465fa72ed gnu: Add biomaRt. 
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
8b7bce740d gnu: Add AnnotationDbi. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
555e3399dc gnu: Add Biobase. 
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
5dfd276602 gnu: edirect: Update to 3.50. 
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
 2016-01-07 11:25:24 +01:00
Ricardo Wurmus
d2540f80c2 gnu: Add and use default IcedTea. 
* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus
43c565d2e7 gnu: Add Jellyfish. 
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
 2016-01-06 11:10:46 +01:00
Ben Woodcroft
19f4554c94 gnu: Add fraggenescan. 
* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
 2015-12-29 20:14:03 -05:00
Ricardo Wurmus
e2cd1d0fb9 gnu: Add GenomicRanges. 
* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus
0e7d5560de gnu: Add XVector. 
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus
bf7764b74f gnu: Add GenomeInfoDb. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus
78addcb0eb gnu: Add IRanges. 
* gnu/packages/bioinformatics.scm (r-iranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus
7485129e4f gnu: Add S4Vectors. 
* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus
d29b25c490 gnu: Add BiocGenerics. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus
9fba89e829 gnu: Add r-acsnminer. 
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
 2015-12-21 17:21:26 +01:00
Ben Woodcroft
02f35bb5a7 gnu: mafft: Update to 7.267. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.
 2015-12-21 15:16:01 +01:00
Ben Woodcroft
5f7e17bef7 gnu: Add snap-aligner. 
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
 2015-12-11 14:34:51 +01:00
Ben Woodcroft
e815c094f7 gnu: python-biopython, python2-biopython: Update to 1.66. 
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
[source]: Use PyPi instead of biopython.org.
 2015-12-10 14:35:56 +01:00
Ricardo Wurmus
b49c5a58dc gnu: preseq: Update to 2.0. 
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
  file.
* gnu-system.am (dist_patch_DATA): Remove them.
 2015-11-20 15:22:06 +01:00
Ricardo Wurmus
c6a24d6e92 gnu: Add smithlab-cpp. 
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
 2015-11-20 15:22:06 +01:00
Ricardo Wurmus
3d51ec919e gnu: edirect: Update home page. 
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
  slash to home page.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
c52a382c4a gnu: sra-tools: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
9e5ef614aa gnu: ncbi-vdb: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
614a8977cb gnu: ngs-java: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
d6a1cd7cae gnu: ngs-sdk: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
9641a89957 gnu: bless: Build only for x86_64. 
* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
 2015-11-20 11:32:32 +01:00
Ricardo Wurmus
0536727efe gnu: htseq: Propagate numpy. 
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
  from here ...
[propagated-inputs]: ... to here.
 2015-11-20 11:32:32 +01:00
Ricardo Wurmus
029d9f77ab gnu: mosaik: Build only on x86_64. 
* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add
  field.
 2015-11-12 12:36:40 +01:00
Ricardo Wurmus
4d75e03ac9 gnu: bless: Correct indentation and home-page. 
* gnu/packages/bioinformatics.scm (bless): Fix indentation.
  [home-page]: Replace broken URL.
 2015-11-06 22:31:29 +01:00
Ricardo Wurmus
6c2b26e21e gnu: Add BLESS. 
* gnu/packages/bioinformatics.scm (bless): New variable.

Co-authored-by: Diane Trout <diane@ghic.org>
 2015-11-06 18:20:50 +01:00
Ricardo Wurmus
60af3d8241 gnu: hisat: Disable build on non-x86_64. 
* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
 2015-11-02 14:37:52 +01:00
Ben Woodcroft
f3674b1c80 gnu: Add express-beta-diversity. 
* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2015-11-02 09:54:21 +01:00
Ricardo Wurmus
9a067efdb2 gnu: pbtranscript-tofu: Update to 2.2.3. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
  [source]: Remove bundled Cython sources in a snippet.  Replace
  ".tar.gz" extension in file-name field with "-checkout".
  [arguments]: Replace "enter-directory-and-clean-up" phase with
  "enter-directory" phase, and add "patch-setuppy" phase.
  [inputs]: Add python2-h5py.  Move python2-cython ...
  [native-inputs]: ... to this field.
 2015-10-28 16:26:58 +01:00
Ricardo Wurmus
104c1986ac gnu: subread: Use SSE optimizations on x86_64 only. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
  CCFLAGS conditionally dependent on target system.
 2015-10-27 12:06:55 +01:00
Ricardo Wurmus
61d5fd03bf gnu: crossmap: Update to 0.2.1. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
 2015-10-27 11:14:13 +01:00
Ricardo Wurmus
fe4c37c244 gnu: Add MOSAIK. 
* gnu/packages/bioinformatics.scm (mosaik): New variable.
 2015-10-22 11:11:09 +02:00
Andreas Enge
ab29be81c5 gnu: ngs-sdk: Correct typo. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Correct typo.
 2015-10-17 22:51:12 +02:00
Andreas Enge
a0dadf0cb1 gnu: ngs-sdk: Remove unsupported systems. 
* gnu/packages/bioinformatics.scm (ngs-sdk)[supported-systems]: Keep only x86
  based systems.
 2015-10-17 22:43:14 +02:00
Ben Woodcroft
d9c44e9c6a gnu: diamond: Restrict supported systems to x86_64-linux. 
* gnu/packages/bioinformatics.scm (diamond) [supported-systems]: Restrict to
  x86_64-linux.
 2015-10-14 20:02:25 +03:00
Ricardo Wurmus
db94f8c734 gnu: bwa: Disable on non-x86_64. 
* gnu/packages/bioinformatics.scm (bwa)[supported-systems]: Add field.
 2015-10-12 15:50:33 +02:00
Ben Woodcroft
6f04e51560 gnu: vsearch: Restrict supported systems to x86_64-linux. 
* gnu/packages/bioinformatics.scm (vsearch)[supported-systems]: Restrict
  to x86_64-linux.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2015-10-03 13:59:11 +02:00
Mark H Weaver
9ab5ea449e gnu: clipper: Add 'file-name' field to source origin. 
* gnu/packages/bioinformatics.scm (clipper)[source]: Add file-name.
 2015-10-02 10:55:57 -04:00
Ben Woodcroft
a2950fa4dc gnu: Add vsearch. 
* gnu/packages/bioinformatics.scm (vsearch): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2015-10-01 10:51:28 +02:00
Pjotr Prins
b2bddb07ef gnu: Add bio-blastxmlparser. 
* gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
 2015-09-28 12:22:47 +02:00
Ludovic Courtès
e1556533d3 Merge branch 'core-updates' 2015-09-26 15:14:53 +02:00
Ben Woodcroft
d708b7a973 gnu: Add seqmagick. 
* gnu/packages/bioinformatics.scm (seqmagick): New variable.
 2015-09-25 16:16:28 +02:00
Mark H Weaver
bd90127ad4 Merge branch 'master' into core-updates 2015-09-22 16:38:48 -04:00
Andreas Enge
a5002ae77c gnu: Add R/qtl. 
* gnu/packages/bioinformatics.scm (r-qtl): New variable.

Co-authored-by: Pjotr Prins <pjotr.guix@thebird.nl>
 2015-09-20 00:32:45 +02:00
Pjotr Prins
edb15985f1 gnu: Add bioruby. 
* gnu/packages/bioinformatics.scm (bioruby): New variable.
 2015-09-19 12:41:52 -04:00
Ben Woodcroft
41ddebdd2a gnu: Add mafft. 
* gnu/packages/bioinformatics.scm (mafft): New variable.
 2015-09-16 23:06:14 +02:00
Pjotr Prins
9c38b54027 gnu: Add bio-locus. 
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
 2015-09-14 12:06:04 -04:00
David Thompson
801a0a2219 Revert "gnu: Add bio-locus." 
This reverts commit b429c4fbb0.
 2015-09-14 12:05:15 -04:00
Pjotr Prins
b429c4fbb0 gnu: Add bio-locus. 
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
 2015-09-14 11:36:30 -04:00
Ludovic Courtès
75710da667 Merge branch 'master' into core-updates 2015-09-13 21:28:01 +02:00
Ricardo Wurmus
1921b1de07 gnu: Add deeptools. 
* gnu/packages/bioinformatics.scm (deeptools): New variable.
 2015-09-02 10:38:43 +02:00
Ludovic Courtès
96c4621056 gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases. 
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
  plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
  Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
 2015-08-29 01:25:08 +02:00
Ricardo Wurmus
f7283db37d gnu: Add BioPerl. 
* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
 2015-08-26 17:54:52 +02:00
Ricardo Wurmus
c1670a8196 gnu: shogun: Move package to machine-learning.scm. 
* gnu/packages/bioinformatics.scm (shogun): Move from here...
* gnu/packages/machine-learning.scm (shogun): ...to here.
 2015-08-14 17:17:05 +02:00
Ben Woodcroft
b81cb1f2f3 gnu: bedtools: Add patch to fix compilation on 32 bit systems. 
* gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
* gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.
* gnu-system.am (dist_patch_DATA): Register patch.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2015-07-25 19:16:49 +02:00
Ben Woodcroft
bd4af2f940 gnu: bedtools: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
 2015-07-25 00:02:54 -04:00
Ben Woodcroft
8dc797fa28 gnu: Add aragorn. 
* gnu/packages/bioinformatics.scm (aragorn): New variable.
 2015-07-21 16:39:38 +02:00
Mark H Weaver
5ede5f2f1c gnu: metabat: Minor tweaks. 
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in
  'fix-includes' phase.
  [license]: Fix misspelling.
 2015-07-19 15:27:15 -04:00
Ben Woodcroft
8fd790eb87 gnu: Add metabat. 
* gnu/packages/bioinformatics.scm (metabat): New variable.
 2015-07-19 15:17:08 -04:00
Ricardo Wurmus
9f04196d88 gnu: preseq: Move "use-samtools-headers" phase. 
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase
  "use-samtools-headers" after "enter-dir" phase.
 2015-07-09 12:12:07 +02:00
Ricardo Wurmus
56e373ef75 gnu: Add preseq. 
* gnu/packages/bioinformatics.scm (preseq): New variable.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add them.
 2015-07-08 17:05:00 +02:00
Ricardo Wurmus
5bdda30b32 gnu: samtools: Install headers. 
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
  "install-headers" to install header files.
 2015-07-08 17:05:00 +02:00
Ricardo Wurmus
795c01f31d gnu: samtools: Update to 1.2. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.2.
 2015-07-07 14:43:07 +02:00
Ben Woodcroft
af86047537 gnu: Add prodigal. 
* gnu/packages/bioinformatics.scm (prodigal): New variable.
 2015-07-05 02:56:53 -04:00
Ricardo Wurmus
151714ca8c gnu: shogun: Build with install RPATH. 
* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to
  build with install RPATH.
 2015-07-04 17:55:30 +02:00
Ricardo Wurmus
c61fe02cc0 gnu: Add WarpedLMM. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
 2015-07-02 11:16:46 +02:00
Ricardo Wurmus
82c370dea1 gnu: Add Blast+. 
* gnu/packages/bioinformatics.scm (blast+): New variable.
 2015-06-29 16:13:28 +02:00
Ricardo Wurmus
cc6ed47737 gnu: Add plink. 
* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
 2015-06-29 12:54:48 +02:00
Ben Woodcroft
c684629f7c gnu: Add hmmer. 
* gnu/packages/bioinformatics.scm (hmmer): New variable.
 2015-06-24 00:39:22 -04:00
Ricardo Wurmus
4758eaaa2d gnu: star: Update to 2.4.2a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.
 2015-06-23 18:37:16 +02:00
Ricardo Wurmus
0ec8b206d4 gnu: miso: Install executables. 
* gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use
  "setuptools" so that executables are built.
* gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock"
  and "python2-pytz".
 2015-06-23 13:13:03 +02:00
Ricardo Wurmus
c4325f6269 gnu: Add idr. 
* gnu/packages/bioinformatics.scm (idr): New variable.
 2015-06-23 10:55:52 +02:00
Ben Woodcroft
12b04cbee6 gnu: Add fasttree. 
* gnu/packages/bioinformatics.scm (fasttree): New variable.
 2015-06-21 03:30:40 -04:00
Ben Woodcroft
684bf7c7f1 gnu: Add diamond. 
* gnu/packages/bioinformatics.scm (diamond): New variable.
 2015-06-17 19:43:54 -04:00
Ricardo Wurmus
86517de69c gnu: miso: Use HTTPS URL. 
* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
  downloading the source tarball.
 2015-06-17 15:28:43 +02:00
Ricardo Wurmus
1bbc3b1d2c gnu: bedops: Update to 2.4.14. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
 2015-06-17 14:37:29 +02:00
Ricardo Wurmus
a98c6eccf8 gnu: orfm: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
 2015-06-15 10:36:42 +02:00
Ben Woodcroft
1e44cf8b0f gnu: Add OrfM. 
* gnu/packages/bioinformatics.scm (orfm): New variable.

Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus
36742f4389 gnu: Add Couger. 
* gnu/packages/bioinformatics.scm (couger): New variable.
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus
e0a02cb21f gnu: ngs-sdk: Update to version 1.1.1. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
 2015-06-12 12:57:29 +02:00
Ricardo Wurmus
e7c097306d gnu: Add HTSlib. 
* gnu/packages/bioinformatics.scm (htslib): New variable.
 2015-06-02 14:30:14 +02:00
Ricardo Wurmus
132b4c8c23 gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
  "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
  i686.
 2015-06-02 14:26:14 +02:00
Ricardo Wurmus
365c815389 gnu: Add edirect. 
* gnu/packages/bioinformatics.scm (edirect): New variable.
 2015-05-27 17:42:40 +02:00
Ricardo Wurmus
628bd9b8a7 gnu: shogun: Remove non-free source files. 
* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove
  non-free sources.
 2015-05-27 10:56:27 +02:00
Ricardo Wurmus
66e3eff1e3 gnu: Add rsem. 
* gnu/packages/bioinformatics.scm (rsem): New variable.
* gnu/packages/patches/rsem-makefile.patch: New file.
 2015-05-22 13:14:29 +02:00
Ricardo Wurmus
7c3958e15a gnu: vcftools: Remove "-m64" from CFLAGS. 
* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to
  remove "-m64" flag.
 2015-05-05 10:20:21 +02:00
Ricardo Wurmus
4702cec246 gnu: bamtools: Set rpath via LDFLAGS. 
* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase
  setting $LDFLAGS to set the rpath to $out/lib/bamtools.
 2015-05-04 11:29:41 +02:00