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496 Commits (93863a5e7257ea074a9a5e3f36a393a8ec29fedf)

Author SHA1 Message Date
Ben Woodcroft 8dec2229a2
gnu: blast+: Update to 2.4.0.
* gnu/packages/bioinformatics.scm (blast+): Update to 2.4.0.
2016-06-29 22:42:47 +10:00
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus ec9466388e
gnu: Add SEEK.
* gnu/packages/bioinformatics.scm (seek): New variable.
2016-06-28 22:49:05 +02:00
Ben Woodcroft d6e374a0d9
gnu: mafft: Update to 7.299.
* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
2016-06-28 21:42:15 +10:00
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 9ded145717
gnu: Add python-screed.
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
2016-06-27 21:16:39 +10:00
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 7b3df1e56e
gnu: Add r-vegan.
* gnu/packages/bioinformatics.scm (r-vegan): New variable.
2016-06-21 21:29:17 +10:00
Ben Woodcroft 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
Ricardo Wurmus 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
Ben Woodcroft e4a44a6aa5
gnu: Add ruby-bio-kseq.
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
2016-06-14 07:57:09 +10:00
Ricardo Wurmus 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
Hartmut Goebel 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
Ben Woodcroft 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
Ricardo Wurmus 64efa3078a
gnu: Add r-genomationdata.
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
2016-05-31 16:29:37 +02:00
Ben Woodcroft 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
Ricardo Wurmus 0783787436 gnu: Add ParDRe.
* gnu/packages/bioinformatics.scm (pardre): New variable.
2016-05-23 12:55:09 +02:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ben Woodcroft 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
Ricardo Wurmus e62ffce538 gnu: Add Piranha.
* gnu/packages/bioinformatics.scm (piranha): New variable.
2016-05-18 11:59:34 +02:00
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Efraim Flashner 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
Mark H Weaver 99828fa788
gnu: Update module imports for asciidoc and doxygen.
This is a followup to commit 0573a923de.

* gnu/packages/algebra.scm, gnu/packages/bioinformatics.scm,
gnu/packages/fcitx.scm, gnu/packages/fish.scm,
gnu/packages/freedesktop.scm, gnu/packages/game-development.scm,
gnu/packages/gcc.scm, gnu/packages/graphics.scm, gnu/packages/image.scm,
gnu/packages/kodi.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/messaging.scm,
gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/rdf.scm,
gnu/packages/serialization.scm, gnu/packages/version-control.scm,
gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xiph.scm: Change imports of (gnu packages asciidoc) or
(gnu packages doxygen) to (gnu packages documentation).
2016-05-12 20:18:15 -04:00
Ricardo Wurmus 83b84fa812 gnu: edirect: Update to 4.10.
* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
2016-05-04 16:45:43 +02:00
Ben Woodcroft 324efb8888 gnu: Add muscle.
* gnu/packages/bioinformatics.scm (muscle): New variable.
2016-04-30 15:46:24 +10:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Roel Janssen 6b49a37e6b gnu: Add filevercmp.
* gnu/packages/bioinformatics.scm (filevercmp): New variable.
2016-04-26 16:41:15 +02:00
Ben Woodcroft 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
Hartmut Goebel 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
Ricardo Wurmus 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
Ricardo Wurmus f94bf1983b gnu: Add python-plastid.
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
  variables.
2016-04-19 12:16:01 +02:00
Ricardo Wurmus 4db9433aa0 gnu: Add python-twobitreader.
* gnu/packages/bioinformatics.scm (python-twobitreader,
  python2-twobitreader): New variables.
2016-04-19 12:16:01 +02:00
Alex Kost 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus ae2462f7dd gnu: Add r-motifrg.
* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
2016-04-11 11:03:27 +02:00
Ricardo Wurmus 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
Ricardo Wurmus 936e7d6774 gnu: Add r-seqlogo.
* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.
2016-04-11 11:03:27 +02:00
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
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
Ricardo Wurmus 0ec8b206d4 gnu: miso: Install executables.
* gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use
  "setuptools" so that executables are built.
* gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock"
  and "python2-pytz".
2015-06-23 13:13:03 +02:00
Ricardo Wurmus c4325f6269 gnu: Add idr.
* gnu/packages/bioinformatics.scm (idr): New variable.
2015-06-23 10:55:52 +02:00
Ben Woodcroft 12b04cbee6 gnu: Add fasttree.
* gnu/packages/bioinformatics.scm (fasttree): New variable.
2015-06-21 03:30:40 -04:00
Ben Woodcroft 684bf7c7f1 gnu: Add diamond.
* gnu/packages/bioinformatics.scm (diamond): New variable.
2015-06-17 19:43:54 -04:00
Ricardo Wurmus 86517de69c gnu: miso: Use HTTPS URL.
* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
  downloading the source tarball.
2015-06-17 15:28:43 +02:00
Ricardo Wurmus 1bbc3b1d2c gnu: bedops: Update to 2.4.14.
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
2015-06-17 14:37:29 +02:00
Ricardo Wurmus a98c6eccf8 gnu: orfm: Update to 0.4.1.
* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
2015-06-15 10:36:42 +02:00
Ben Woodcroft 1e44cf8b0f gnu: Add OrfM.
* gnu/packages/bioinformatics.scm (orfm): New variable.

Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
2015-06-12 12:57:30 +02:00
Ricardo Wurmus 36742f4389 gnu: Add Couger.
* gnu/packages/bioinformatics.scm (couger): New variable.
2015-06-12 12:57:30 +02:00
Ricardo Wurmus e0a02cb21f gnu: ngs-sdk: Update to version 1.1.1.
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
2015-06-12 12:57:29 +02:00
Ricardo Wurmus e7c097306d gnu: Add HTSlib.
* gnu/packages/bioinformatics.scm (htslib): New variable.
2015-06-02 14:30:14 +02:00
Ricardo Wurmus 132b4c8c23 gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
  "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
  i686.
2015-06-02 14:26:14 +02:00
Ricardo Wurmus 365c815389 gnu: Add edirect.
* gnu/packages/bioinformatics.scm (edirect): New variable.
2015-05-27 17:42:40 +02:00
Ricardo Wurmus 628bd9b8a7 gnu: shogun: Remove non-free source files.
* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove
  non-free sources.
2015-05-27 10:56:27 +02:00
Ricardo Wurmus 66e3eff1e3 gnu: Add rsem.
* gnu/packages/bioinformatics.scm (rsem): New variable.
* gnu/packages/patches/rsem-makefile.patch: New file.
2015-05-22 13:14:29 +02:00
Ricardo Wurmus 7c3958e15a gnu: vcftools: Remove "-m64" from CFLAGS.
* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to
  remove "-m64" flag.
2015-05-05 10:20:21 +02:00
Ricardo Wurmus 4702cec246 gnu: bamtools: Set rpath via LDFLAGS.
* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase
  setting $LDFLAGS to set the rpath to $out/lib/bamtools.
2015-05-04 11:29:41 +02:00
Ricardo Wurmus 0b84a0aaca gnu: Add samtools-0.1.19.
* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
2015-05-04 10:28:27 +02:00