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
69e0e03c36
gnu: Add python-pybigwig.
...
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
New variables.
2016-03-03 13:46:52 +01:00
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
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
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
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
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
d1e32822b4
gnu: Add PePr.
...
* gnu/packages/bioinformatics.scm (pepr): New variable.
2016-03-01 11:51:24 +01:00
d29150b55d
gnu: Add bwa-pssm.
...
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
2016-03-01 10:31:04 +01:00
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
736f9ffce2
gnu: Add missing import in bioinformatics.scm.
...
This is a followup to 1baee94
2016-02-25 12:48:08 +01:00
1baee943ca
gnu: Add libBigWig.
...
* gnu/packages/bioinformatics.scm (libbigwig): New variable.
2016-02-25 11:43:44 +01:00
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
d1dbde6ac1
gnu: Add r-graph.
...
* gnu/packages/bioinformatics.scm (r-graph): New variable.
2016-02-24 17:36:55 +01:00
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
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
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
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
578b05d99e
gnu: htseq: Add PySam to inputs.
...
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".
2016-02-16 15:32:15 +01:00
d15d981ea2
gnu: Add StringTie.
...
* gnu/packages/bioinformatics.scm (stringtie): New variable.
2016-02-16 14:51:10 +01:00
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
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
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
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
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
ce294c0445
gnu: Update sortmerna to 2.1.
...
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
2016-02-02 22:42:38 +10:00
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
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
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
bcadaf0050
gnu: Add sortmerna.
...
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
2016-01-25 08:35:11 +10:00
3a40a92c73
gnu: Add cufflinks.
...
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
2016-01-23 09:15:11 +01:00
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
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
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
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
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
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
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
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
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
81f3e0c1f3
gnu: Add fxtract.
...
* gnu/packages/bioinformatics.scm (fxtract): New variable.
2016-01-12 07:49:19 +10:00
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
6573ac82ad
gnu: bedtools: Use modify-phases.
...
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2016-01-11 00:36:13 +10:00
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
cb933df6da
gnu: Add genomation.
...
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
2016-01-07 17:18:17 +01:00
03ea5a357e
gnu: Add seqPattern.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
2016-01-07 17:18:17 +01:00
c43a011de3
gnu: Add impute.
...
* gnu/packages/bioinformatics.scm (r-impute): New variable.
2016-01-07 17:18:17 +01:00
c63cef6699
gnu: Add BSgenome.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
2016-01-07 17:18:17 +01:00
d547ce5e70
gnu: Add topGO.
...
* gnu/packages/bioinformatics.scm (r-topgo): New variable.
2016-01-07 17:18:17 +01:00
fb25d8803f
gnu: Add GO.db.
...
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
2016-01-07 17:18:16 +01:00
2fd7c04984
gnu: Add GenomicFeatures.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
2016-01-07 17:18:16 +01:00
317755ff0f
gnu: Add rtracklayer.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
2016-01-07 17:18:16 +01:00
d8a828af78
gnu: Add GenomicAlignments.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
2016-01-07 17:18:16 +01:00
6e76dda2d0
gnu: Add SummarizedExperiment.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
2016-01-07 17:18:16 +01:00
f8d74f7018
gnu: Add Rsamtools.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
2016-01-07 17:18:16 +01:00
bf15935337
gnu: Add Biostrings.
...
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
2016-01-07 17:18:16 +01:00
e91d362e48
gnu: Add BiocParallel.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
2016-01-07 17:18:16 +01:00
c465fa72ed
gnu: Add biomaRt.
...
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
2016-01-07 17:18:16 +01:00
8b7bce740d
gnu: Add AnnotationDbi.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
2016-01-07 17:18:16 +01:00
555e3399dc
gnu: Add Biobase.
...
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
2016-01-07 17:18:16 +01:00
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
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
43c565d2e7
gnu: Add Jellyfish.
...
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
2016-01-06 11:10:46 +01:00
19f4554c94
gnu: Add fraggenescan.
...
* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
2015-12-29 20:14:03 -05:00
e2cd1d0fb9
gnu: Add GenomicRanges.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
2015-12-21 17:22:16 +01:00
0e7d5560de
gnu: Add XVector.
...
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
2015-12-21 17:22:16 +01:00
bf7764b74f
gnu: Add GenomeInfoDb.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
2015-12-21 17:22:16 +01:00
78addcb0eb
gnu: Add IRanges.
...
* gnu/packages/bioinformatics.scm (r-iranges): New variable.
2015-12-21 17:22:16 +01:00
7485129e4f
gnu: Add S4Vectors.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
2015-12-21 17:22:16 +01:00
d29b25c490
gnu: Add BiocGenerics.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
2015-12-21 17:22:16 +01:00
9fba89e829
gnu: Add r-acsnminer.
...
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
2015-12-21 17:21:26 +01:00
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
5f7e17bef7
gnu: Add snap-aligner.
...
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
2015-12-11 14:34:51 +01:00
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
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
c6a24d6e92
gnu: Add smithlab-cpp.
...
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
2015-11-20 15:22:06 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
fe4c37c244
gnu: Add MOSAIK.
...
* gnu/packages/bioinformatics.scm (mosaik): New variable.
2015-10-22 11:11:09 +02:00
ab29be81c5
gnu: ngs-sdk: Correct typo.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Correct typo.
2015-10-17 22:51:12 +02:00
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
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
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
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
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
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
b2bddb07ef
gnu: Add bio-blastxmlparser.
...
* gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
2015-09-28 12:22:47 +02:00
Ricardo Wurmus