3bce0f14b2
gnu: star: Update to 2.5.2a.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.5.2a.
2016-06-29 10:14:22 +10:00
6c737963f6
gnu: htslib: Update to 1.3.1.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.3.1.
2016-06-29 10:14:22 +10:00
ec9466388e
gnu: Add SEEK.
...
* gnu/packages/bioinformatics.scm (seek): New variable.
2016-06-28 22:49:05 +02:00
d6e374a0d9
gnu: mafft: Update to 7.299.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
2016-06-28 21:42:15 +10:00
45469ebe52
gnu: metabat: Update to 0.26.3.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3.
[arguments]: Update include and linking paths accordingly.
2016-06-28 21:28:06 +10:00
af45244e36
gnu: diamond: Update to 0.8.9.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.9.
2016-06-28 19:31:25 +10:00
94ff31572d
gnu: Add khmer.
...
* gnu/packages/bioinformatics.scm (khmer): New variable.
* gnu/packages/patches/khmer-use-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-06-27 21:35:16 +10:00
9ded145717
gnu: Add python-screed.
...
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
2016-06-27 21:16:39 +10:00
c2e575185b
gnu: vsearch: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.0.
2016-06-26 12:43:39 +10:00
69af462496
gnu: vsearch: Update to 0.11.2.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 0.11.2.
2016-06-22 07:51:12 +10:00
7b3df1e56e
gnu: Add r-vegan.
...
* gnu/packages/bioinformatics.scm (r-vegan): New variable.
2016-06-21 21:29:17 +10:00
cec2653bb4
gnu: diamond: Update to 0.8.7.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.7.
2016-06-21 20:00:38 +10:00
4714d521e3
gnu: Add r-bsgenome-mmusculus-ucsc-mm10.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
variable.
2016-06-15 17:08:08 +02:00
e4a44a6aa5
gnu: Add ruby-bio-kseq.
...
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
2016-06-14 07:57:09 +10:00
883302daf2
gnu: piranha: Update to 1.2.1.
...
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
2016-06-13 11:53:38 +02:00
698bd29799
gnu: Use full SHA1 commit ids.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu, mosaik,
smithlab-cpp, piranha): Use full SHA1 commit ids.
* gnu/packages/ci.scm (hydra): Likewise.
* gnu/packages/compression.scm (sfarkxtc): Likewise.
* gnu/packages/emacs.scm (emacs-ob-ipython): Likewise.
* gnu/packages/games.scm (mars, emulation-station): Likewise.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/music.scm (non-sequencer): Likewise.
* gnu/packages/version-control.scm (git-flow, git-test-sequence): Likewise.
* gnu/packages/xorg.scm (xf86-video-intel): Likewise.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-06-05 00:05:38 +02:00
6ac0a0fbe7
gnu: diamond: Update to 0.8.5.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5.
2016-06-04 09:28:54 +10:00
64efa3078a
gnu: Add r-genomationdata.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
2016-05-31 16:29:37 +02:00
9fcc3509a7
gnu: Update diamond to 0.8.3.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
2016-05-28 23:44:16 +10:00
0783787436
gnu: Add ParDRe.
...
* gnu/packages/bioinformatics.scm (pardre): New variable.
2016-05-23 12:55:09 +02:00
7740f58128
gnu: r-genomation: Update to 1.4.2.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
2016-05-20 15:18:23 +02:00
8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
2016-05-20 15:18:23 +02:00
192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
2016-05-20 15:18:23 +02:00
d7420566a9
gnu: r-biocparallel: Update to 1.6.2.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
2016-05-20 15:18:23 +02:00
73af676feb
gnu: r-annotationdbi: Update to 1.34.2.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
2016-05-20 15:18:23 +02:00
679e670b36
gnu: r-variantannotation: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
2016-05-20 15:18:23 +02:00
186ed87337
gnu: r-genomeinfodb: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
2016-05-20 15:18:23 +02:00
7c544991dc
gnu: diamond: Do not specify target architecture.
...
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
2016-05-18 21:25:06 +10:00
e62ffce538
gnu: Add Piranha.
...
* gnu/packages/bioinformatics.scm (piranha): New variable.
2016-05-18 11:59:34 +02:00
849485f5a0
gnu: sortmerna: Update to 2.1b.
...
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
2016-05-17 21:45:49 +10:00
daaeed765a
gnu: vsearch: Update to 1.11.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
2016-05-17 21:36:46 +10:00
122395f9fc
gnu: diamond: Update to 0.8.1.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
2016-05-17 21:07:00 +10:00
96101b6718
gnu: r-zlibbioc: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
2016-05-16 20:59:50 +02:00
a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
2016-05-16 20:59:38 +02:00
1f5786a918
gnu: r-seqlogo: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
2016-05-16 20:59:27 +02:00
8adc3b628d
gnu: r-genomation: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
2016-05-16 20:59:14 +02:00
7555817c2b
gnu: r-seqpattern: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
2016-05-16 20:59:04 +02:00
d1bff89d26
gnu: r-impute: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
2016-05-16 20:58:49 +02:00
5190ed1751
gnu: r-bsgenome: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
2016-05-16 20:58:35 +02:00
e48e88c217
gnu: r-topgo: Update to 2.24.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0.
[propagated-inputs]: Add r-matrixstats.
2016-05-16 20:58:24 +02:00
0c56023557
gnu: r-graph: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
2016-05-16 20:58:08 +02:00
c12b0a5a30
gnu: r-genomicfeatures: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
2016-05-16 20:57:55 +02:00
d23fbf1eb9
gnu: r-rtracklayer: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
2016-05-16 20:57:43 +02:00
3cd551ea7b
gnu: r-genomicalignments: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
2016-05-16 20:57:30 +02:00
d848ed7cf2
gnu: r-summarizedexperiment: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
2016-05-16 20:57:21 +02:00
b4c5a0db22
gnu: r-rsamtools: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
2016-05-16 20:57:10 +02:00
2477d9773a
gnu: r-biostrings: Update to 2.40.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
2016-05-16 20:56:58 +02:00
6a2a0de1ab
gnu: r-biocparallel: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
2016-05-16 20:56:39 +02:00
63cea37234
gnu: r-biomart: Update to 2.28.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
2016-05-16 20:56:29 +02:00
c4a4e17938
gnu: r-annotationdbi: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
2016-05-16 20:56:19 +02:00
4466a02c9f
gnu: r-biobase: Update to 2.32.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
2016-05-16 20:56:09 +02:00
828980cad6
gnu: r-genomicranges: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
2016-05-16 20:55:58 +02:00
e782ca3e97
gnu: r-xvector: Update to 0.12.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
2016-05-16 20:55:46 +02:00
052ee32b24
gnu: r-variantannotation: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.18.0.
2016-05-16 20:55:32 +02:00
d1ab3d8fa5
gnu: r-genomeinfodb: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
2016-05-16 20:55:20 +02:00
952ff8c862
gnu: r-iranges: Update to 2.6.0.
...
* gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
2016-05-16 20:55:11 +02:00
3654a61146
gnu: r-s4vectors: Update to 0.10.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
2016-05-16 20:54:59 +02:00
a936bf59ea
gnu: r-dnacopy: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
2016-05-16 20:54:37 +02:00
dbfeba5209
gnu: r-biocgenerics: Update to 0.18.0.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
2016-05-16 20:53:48 +02:00
a83e604662
gnu: hmmer: Update urls.
...
* gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to
eddylab, with their downloads.
[home-page]: Update to new homepage.
2016-05-16 14:28:53 +03:00
99828fa788
gnu: Update module imports for asciidoc and doxygen.
...
This is a followup to commit 0573a923de
2016-05-12 20:18:15 -04:00
83b84fa812
gnu: edirect: Update to 4.10.
...
* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
2016-05-04 16:45:43 +02:00
324efb8888
gnu: Add muscle.
...
* gnu/packages/bioinformatics.scm (muscle): New variable.
2016-04-30 15:46:24 +10:00
fb868e3395
gnu: r-acsnminer: Update to 0.16.01.29.
...
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.01.29.
2016-04-26 17:06:17 +02:00
e1c2ad6777
gnu: r-qtl: Update to 1.39-5.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.39-5.
2016-04-26 17:06:17 +02:00
6b49a37e6b
gnu: Add filevercmp.
...
* gnu/packages/bioinformatics.scm (filevercmp): New variable.
2016-04-26 16:41:15 +02:00
79b555edeb
gnu: samtools: Update to 1.3.1.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
2016-04-24 09:45:07 +10:00
1ad15c1669
gnu: Rename Java packages to match new naming specification.
...
* gnu/packages/bioinformatics.scm (htsjdk): Rename to...
(java-htsjdk): ...this.
(ngs-java): Rename to...
(java-ngs): ...this.
(ncbi-vdb)[arguments,inputs]: Use new name.
* gnu/packages/java.scm (swt): Rename to...
(java-swt): ...this.
* gnu/packages/music.scm (tuxguitar)[make-flags,inputs,arguments]: Use
new name of package "swt".
2016-04-19 16:55:03 +02:00
4d16cc5133
gnu: python2-plastid: Propagate setuptools.
...
* gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move
python2-setuptools from here...
[propagated-inputs]: ...to here.
2016-04-19 16:12:51 +02:00
f94bf1983b
gnu: Add python-plastid.
...
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
variables.
2016-04-19 12:16:01 +02:00
4db9433aa0
gnu: Add python-twobitreader.
...
* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader): New variables.
2016-04-19 12:16:01 +02:00
fc1adab148
gnu: packages: Use 'search-patches' everywhere.
...
* gnu/packages/abiword.scm: Use 'search-patches' for 'patches' field.
* gnu/packages/acl.scm: Likewise.
* gnu/packages/admin.scm: Likewise.
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/animation.scm: Likewise.
* gnu/packages/apr.scm: Likewise.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/autotools.scm: Likewise.
* gnu/packages/avahi.scm: Likewise.
* gnu/packages/backup.scm: Likewise.
* gnu/packages/base.scm: Likewise.
* gnu/packages/bash.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/ci.scm: Likewise.
* gnu/packages/cmake.scm: Likewise.
* gnu/packages/cpio.scm: Likewise.
* gnu/packages/cross-base.scm: Likewise.
* gnu/packages/dico.scm: Likewise.
* gnu/packages/doxygen.scm: Likewise.
* gnu/packages/ebook.scm: Likewise.
* gnu/packages/elf.scm: Likewise.
* gnu/packages/emacs.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/ftp.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gawk.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gd.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/gnunet.scm: Likewise.
* gnu/packages/gnupg.scm: Likewise.
* gnu/packages/gnuzilla.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/grub.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/icu4c.scm: Likewise.
* gnu/packages/idutils.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/imagemagick.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/ldc.scm: Likewise.
* gnu/packages/libcanberra.scm: Likewise.
* gnu/packages/libevent.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libunwind.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/llvm.scm: Likewise.
* gnu/packages/lsh.scm: Likewise.
* gnu/packages/lua.scm: Likewise.
* gnu/packages/lxqt.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/mit-krb5.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/ninja.scm: Likewise.
* gnu/packages/nvi.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/orpheus.scm: Likewise.
* gnu/packages/ots.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/patchutils.scm: Likewise.
* gnu/packages/pcre.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/polkit.scm: Likewise.
* gnu/packages/pulseaudio.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/qemu.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/ratpoison.scm: Likewise.
* gnu/packages/rdf.scm: Likewise.
* gnu/packages/readline.scm: Likewise.
* gnu/packages/rush.scm: Likewise.
* gnu/packages/scheme.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/sdl.scm: Likewise.
* gnu/packages/slim.scm: Likewise.
* gnu/packages/ssh.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/tcsh.scm: Likewise.
* gnu/packages/texinfo.scm: Likewise.
* gnu/packages/tls.scm: Likewise.
* gnu/packages/tor.scm: Likewise.
* gnu/packages/tv.scm: Likewise.
* gnu/packages/valgrind.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vtk.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wicd.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.
* gnu/packages/xiph.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.
* gnu/packages/zip.scm: Likewise.
2016-04-14 10:38:21 +03:00
6dc6099853
gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
New variable.
2016-04-11 15:11:16 +02:00
943bd6279f
gnu: Add r-bsgenome-celegans-ucsc-ce6.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New
variable.
2016-04-11 15:11:16 +02:00
a3e9028770
gnu: Add r-bsgenome-mmusculus-ucsc-mm9.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New
variable.
2016-04-11 15:11:15 +02:00
ae2462f7dd
gnu: Add r-motifrg.
...
* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
2016-04-11 11:03:27 +02:00
c90a4baff6
gnu: Add r-bsgenome-hsapiens-ucsc-hg19.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New
variable.
2016-04-11 11:03:27 +02:00
936e7d6774
gnu: Add r-seqlogo.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.
2016-04-11 11:03:27 +02:00
9e3ba31c53
gnu: Add r-zlibbioc.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-06 17:38:42 -04:00
b669d9c4c8
gnu: Add r-variantannotation.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-06 17:38:42 -04:00
9b36e25607
gnu: vcftools: Update to 0.1.14.
...
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[arguments]: Do not modify phases as it is not needed anymore.
[native-inputs]: Add 'pkg-config'.
[home-page]: Update to new location.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-04-05 11:29:32 +03:00
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
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
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
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
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
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
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
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
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
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
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
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
6c1305f9ec
gnu: Add CD-HIT.
...
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
2016-03-17 13:01:31 +01:00
247d498aaa
gnu: Add r-dnacopy.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.
2016-03-16 11:23:27 +01:00
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
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
846e340954
gnu: Add pyicoteo.
...
* gnu/packages/bioinformatics.scm (pyicoteo): New variable.
2016-03-14 12:36:49 +01:00
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
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
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
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
e1556533d3
Merge branch 'core-updates'
2015-09-26 15:14:53 +02:00
d708b7a973
gnu: Add seqmagick.
...
* gnu/packages/bioinformatics.scm (seqmagick): New variable.
2015-09-25 16:16:28 +02:00
bd90127ad4
Merge branch 'master' into core-updates
2015-09-22 16:38:48 -04:00
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
edb15985f1
gnu: Add bioruby.
...
* gnu/packages/bioinformatics.scm (bioruby): New variable.
2015-09-19 12:41:52 -04:00
41ddebdd2a
gnu: Add mafft.
...
* gnu/packages/bioinformatics.scm (mafft): New variable.
2015-09-16 23:06:14 +02:00
9c38b54027
gnu: Add bio-locus.
...
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
2015-09-14 12:06:04 -04:00
801a0a2219
Revert "gnu: Add bio-locus."
...
This reverts commit b429c4fbb0
2015-09-14 12:05:15 -04:00
b429c4fbb0
gnu: Add bio-locus.
...
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
2015-09-14 11:36:30 -04:00
75710da667
Merge branch 'master' into core-updates
2015-09-13 21:28:01 +02:00
1921b1de07
gnu: Add deeptools.
...
* gnu/packages/bioinformatics.scm (deeptools): New variable.
2015-09-02 10:38:43 +02:00
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
f7283db37d
gnu: Add BioPerl.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
2015-08-26 17:54:52 +02:00
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
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
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
8dc797fa28
gnu: Add aragorn.
...
* gnu/packages/bioinformatics.scm (aragorn): New variable.
2015-07-21 16:39:38 +02:00
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
8fd790eb87
gnu: Add metabat.
...
* gnu/packages/bioinformatics.scm (metabat): New variable.
2015-07-19 15:17:08 -04:00
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
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
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
795c01f31d
gnu: samtools: Update to 1.2.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.2.
2015-07-07 14:43:07 +02:00
af86047537
gnu: Add prodigal.
...
* gnu/packages/bioinformatics.scm (prodigal): New variable.
2015-07-05 02:56:53 -04:00
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
c61fe02cc0
gnu: Add WarpedLMM.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
2015-07-02 11:16:46 +02:00
82c370dea1
gnu: Add Blast+.
...
* gnu/packages/bioinformatics.scm (blast+): New variable.
2015-06-29 16:13:28 +02:00
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
c684629f7c
gnu: Add hmmer.
...
* gnu/packages/bioinformatics.scm (hmmer): New variable.
2015-06-24 00:39:22 -04:00
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
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
c4325f6269
gnu: Add idr.
...
* gnu/packages/bioinformatics.scm (idr): New variable.
2015-06-23 10:55:52 +02:00
12b04cbee6
gnu: Add fasttree.
...
* gnu/packages/bioinformatics.scm (fasttree): New variable.
2015-06-21 03:30:40 -04:00
684bf7c7f1
gnu: Add diamond.
...
* gnu/packages/bioinformatics.scm (diamond): New variable.
2015-06-17 19:43:54 -04:00
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
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
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
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
36742f4389
gnu: Add Couger.
...
* gnu/packages/bioinformatics.scm (couger): New variable.
2015-06-12 12:57:30 +02:00
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
e7c097306d
gnu: Add HTSlib.
...
* gnu/packages/bioinformatics.scm (htslib): New variable.
2015-06-02 14:30:14 +02:00
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
365c815389
gnu: Add edirect.
...
* gnu/packages/bioinformatics.scm (edirect): New variable.
2015-05-27 17:42:40 +02:00
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
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
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
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
0b84a0aaca
gnu: Add samtools-0.1.19.
...
* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
2015-05-04 10:28:27 +02:00
41dd712657
gnu: samtools: Install libbam.a library.
...
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-library" to install the libbam.a library.
2015-05-04 10:28:26 +02:00
0a75450c14
gnu: samtools: Remove patch-makefile-curses phase.
...
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
patch-makefile-curses phase, use make-flags instead.
2015-05-04 10:28:26 +02:00
4ca009c036
gnu: flexbar: Enable tests.
...
* gnu/packages/bioinformatics.scm (flexbar): Enable tests.
2015-04-27 15:12:47 +02:00
e4e5a4d88f
gnu: Add eXpress.
...
* gnu/packages/bioinformatics.scm (express): New variable.
2015-04-21 17:57:22 +02:00
9794180d5e
gnu: Add bamtools.
...
* gnu/packages/bioinformatics.scm (bamtools): New variable.
2015-04-21 17:57:22 +02:00
dbf4ed7c91
gnu: Add subread.
...
* gnu/packages/bioinformatics.scm (subread): New variable.
2015-04-21 10:46:23 +02:00
51c649992e
gnu: Add sra-tools.
...
* gnu/packages/bioinformatics.scm (sra-tools): New variable.
2015-04-20 15:29:17 +02:00
75dd242480
gnu: Add NCBI VDB.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
2015-04-20 15:29:17 +02:00
2651a5e695
gnu: Add NGS Java bindings.
...
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
2015-04-20 15:29:16 +02:00
282c5087b4
gnu: Add NGS SDK.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
2015-04-20 15:28:58 +02:00
85c37e29a4
gnu: Add Biopython.
...
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
variables.
2015-04-20 15:23:23 +02:00
2127cedb23
gnu: Add FASTX Toolkit.
...
* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
2015-04-16 10:28:37 +02:00
8214b7fbea
gnu: rseqc: Update hash.
...
* gnu/packages/bioinformatics.scm (rseqc): Update hash.
2015-04-13 15:39:02 +02:00
5854f6858b
gnu: Add GRIT.
...
* gnu/packages/bioinformatics.scm (grit): New variable.
2015-04-10 14:35:48 +02:00
c833ab556f
gnu: Add Shogun.
...
* gnu/packages/bioinformatics.scm (shogun): New variable.
2015-04-09 15:05:12 +02:00
bfe3c68572
gnu: Add clustal omega.
...
* gnu/packages/bioinformatics.scm (clustal-omega): New variable.
2015-04-01 11:39:39 +02:00
c5372108f2
gnu: pbtranscript-tofu: Add missing inputs.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
runtime inputs.
2015-03-31 20:04:41 +02:00
49261e45d8
gnu: pbtranscript-tofu: Delete pre-built libraries.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
"build" directory and any shared objects after unpacking.
2015-03-31 20:04:32 +02:00
de07c0db4a
gnu: Add vcftools.
...
* gnu/packages/bioinformatics.scm (vcftools): New variable.
2015-03-31 17:43:52 +02:00
8e913213d9
gnu: Add cutadapt.
...
* gnu/packages/bioinformatics.scm (cutadapt): New variable.
2015-03-31 17:38:56 +02:00
2c16316ef4
gnu: Add pbtranscript-tofu.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
2015-03-24 16:59:47 +01:00
ad641d53de
gnu: Add python2-bx-python.
...
* gnu/packages/bioinformatics.scm (python2-bx-python): New variable.
2015-03-24 15:00:09 +01:00
19ee920144
gnu: Add python2-pbcore.
...
* gnu/packages/bioinformatics.scm (python2-pbcore): New variable.
2015-03-24 14:58:47 +01:00
ddd82e0e76
gnu: Add MISO.
...
* gnu/packages/bioinformatics.scm (miso): New variable.
2015-03-17 12:29:58 +01:00
9a8336d87b
gnu: Add bwa.
...
* gnu/packages/bioinformatics.scm (bwa): New variable.
2015-03-17 12:29:51 +01:00
15a3c3d4f1
gnu: Add htsjdk.
...
* gnu/packages/bioinformatics.scm (htsjdk): New variable.
2015-03-10 11:46:49 +01:00
1289062522
Merge branch 'core-updates'.
2015-03-04 14:07:23 +01:00
191c710139
gnu: Add crossmap.
...
* gnu/packages/bioinformatics.scm (crossmap): New variable.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2015-03-02 17:23:56 +01:00
810cff8557
gnu: Add CLIPper.
...
* gnu/packages/bioinformatics.scm (clipper): New variable.
2015-03-02 14:11:54 +01:00
d57e6d0f8e
gnu: Add MACS.
...
* gnu/packages/bioinformatics.scm (macs): New variable.
2015-03-02 11:33:13 +01:00
a2fb1492af
gnu: Add pybedtools.
...
* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
2015-03-02 11:32:10 +01:00
f586c87705
gnu: Add 'file-name' fields for github source tarballs without a name.
...
* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb),
gnu/packages/audio.scm (jack-2, lvtk),
gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie),
gnu/packages/game-development.scm (tiled),
gnu/packages/games.scm (minetest-data, minetest, retroarch),
gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson),
gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask),
gnu/packages/mail.scm (offlineimap, libetpan),
gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja),
gnu/packages/nutrition.scm (gourmet),
gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf),
gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add
'file-name' field to origin.
2015-02-28 09:49:01 -05:00
da6dd842d0
gnu: Remove now unneeded 'unpack' phases for unzip.
...
This is a followup to commit cd0385b
2015-02-27 15:08:37 +01:00
85652f599a
gnu: Add HTSeq.
...
* gnu/packages/bioinformatics.scm (htseq): New variable.
2015-02-20 19:31:53 +01:00
8622a07280
gnu: Add RSeQC.
...
* gnu/packages/bioinformatics.scm (rseqc): New variable.
2015-02-19 13:41:38 +01:00
8dd4ff1133
gnu: Add bedops.
...
* gnu/packages/bioinformatics.scm (bedops): New variable.
2015-02-13 15:51:10 +01:00
e58d01faf5
gnu: hisat: fix build on non-x86_64.
...
* gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to
make-flags on architectures other than x86_64.
2015-02-12 14:09:00 +01:00
ce7155d5dd
gnu: Add STAR.
...
* gnu/packages/bioinformatics.scm (star): New variable.
2015-02-10 14:37:14 +01:00
346a829a85
gnu: Add HISAT.
...
* gnu/packages/bioinformatics.scm (hisat): New variable.
2015-02-10 14:37:13 +01:00
d7678942f9
gnu: Add flexbar.
...
* gnu/packages/bioinformatics.scm (flexbar): New variable.
2015-02-09 10:26:28 +01:00
d3517eda25
gnu: Add seqan.
...
* gnu/packages/bioinformatics.scm (seqan): New variable.
2015-02-09 10:26:20 +01:00
241e122193
gnu: bowtie: fix build errors
...
* gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and
add Makefile patch.
* gnu/packages/patches/bowtie-fix-makefile.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2015-01-30 10:45:27 +01:00
2c7ee16720
gnu: Add bowtie
...
* gnu/packages/bioinformatics.scm (bowtie): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-19 18:50:28 +01:00
81de56479a
gnu: Add bedtools
...
* gnu/packages/bioinformatics.scm (bedtools): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-16 18:17:15 +01:00
f3cd952b45
gnu: samtools: disable tests for non-64-bit systems
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* gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
systems because of an upstream bug in the test data.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-16 18:17:15 +01:00
4e10a22168
gnu: Add samtools
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* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-13 00:01:06 +01:00
Ben Woodcroft