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314 Commits

Author SHA1 Message Date
Efraim Flashner ddb8312911 gnu: python2-pbcore: Update to 1.2.8. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.8.
[native-inputs]: Add python2-docutils, python2-nose, python2-sphinx.
 2016-03-30 22:45:35 +03:00
Ricardo Wurmus f315f4fcab gnu: r-genomation: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.2.2.
 2016-03-30 11:59:16 +02:00
Ricardo Wurmus 571f0b63d5 gnu: r-genomicfeatures: Update to 1.22.13. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to
  1.22.13.
 2016-03-30 11:59:16 +02:00
Ricardo Wurmus ffaf72ad96 gnu: r-rtracklayer: Update to 1.30.4. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.30.4.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus ac2d8b0fb8 gnu: r-genomicalignments: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
  1.6.3.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 7eade1c5f9 gnu: r-summarizedexperiment: Update to 1.0.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
  1.0.2.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 53fd0f5e1d gnu: r-biostrings: Update to 2.38.4. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.38.4.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 5fe3115415 gnu: r-genomicranges: Update to 1.22.4. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.22.4.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 9cc22d28d8 gnu: r-genomeinfodb: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.6.3.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 1d216b6ec9 gnu: Remove "r-repository" property. 
* gnu/packages/bioinformatics.scm (r-biocgenerics, r-s4vectors,
r-iranges, r-genomeinfodb, r-xvector, r-genomicranges)[properties]:
Remove "r-repository" property.
 2016-03-24 16:18:01 +01:00
Ludovic Courtès 5697fdc366 gnu: r-dnacopy: Fix home page URL. 
* gnu/packages/bioinformatics.scm (r-dnacopy)[home-page]: Add missing
URI scheme.
 2016-03-18 23:00:04 +01:00
Ricardo Wurmus 953c12232f gnu: bless: Remove bundled sources for sparsehash. 
* gnu/packages/bioinformatics.scm (bless)[source]: Delete
"google-sparsehash" sources.
[inputs]: Add "sparsehash".
 2016-03-17 13:01:31 +01:00
Ricardo Wurmus 6c1305f9ec gnu: Add CD-HIT. 
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
 2016-03-17 13:01:31 +01:00
Roel Janssen 247d498aaa gnu: Add r-dnacopy. 
* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.
 2016-03-16 11:23:27 +01:00
Rob Syme 6a35566df7 gnu: Add codingquarry. 
* gnu/packages/bioinformatics.scm (codingquarry): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-03-16 04:49:27 -04:00
Ricardo Wurmus 10b4a969be gnu: htsjdk: Use ant-build-system. 
* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use
ant-build-system.
[arguments]: Adapt for ant-build-system.
 2016-03-14 14:30:03 +01:00
Ricardo Wurmus 846e340954 gnu: Add pyicoteo. 
* gnu/packages/bioinformatics.scm (pyicoteo): New variable.
 2016-03-14 12:36:49 +01:00
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