| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: r-go-db: Bioconductor changed URL for data downloads.•••* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
| Pjotr Prins | 2016-03-01 | 1 | -1/+3 |
| * | gnu: r-iranges: Update to 2.4.8.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
| Pjotr Prins | 2016-03-01 | 1 | -2/+2 |
| * | gnu: r-s4vectors: Update to 0.8.11.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
| Pjotr Prins | 2016-03-01 | 1 | -4/+3 |
| * | gnu: Add PePr.•••* gnu/packages/bioinformatics.scm (pepr): New variable.
| Ricardo Wurmus | 2016-03-01 | 1 | -0/+41 |
| * | gnu: Add bwa-pssm.•••* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
| Ricardo Wurmus | 2016-03-01 | 1 | -0/+30 |
| * | 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).
| Mark H Weaver | 2016-02-27 | 1 | -1/+1 |
| * | gnu: Add missing import in bioinformatics.scm.•••This is a followup to 1baee94.
* gnu/packages/bioinformatics.scm: Add missing import.
| Ludovic Courtès | 2016-02-25 | 1 | -0/+1 |
| * | gnu: Add libBigWig.•••* gnu/packages/bioinformatics.scm (libbigwig): New variable.
| Ricardo Wurmus | 2016-02-25 | 1 | -0/+47 |
| * | gnu: r-topgo: Add missing input.•••* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add
"r-graph".
| Ricardo Wurmus | 2016-02-24 | 1 | -0/+1 |
| * | gnu: Add r-graph.•••* gnu/packages/bioinformatics.scm (r-graph): New variable.
| Ricardo Wurmus | 2016-02-24 | 1 | -0/+19 |
| * | gnu: Add r-org-mm-eg-db.•••* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable.
| Ricardo Wurmus | 2016-02-24 | 1 | -0/+26 |
| * | gnu: Add r-org-dm-eg-db.•••* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.
| Ricardo Wurmus | 2016-02-24 | 1 | -0/+26 |
| * | gnu: Add r-org-ce-eg-db.•••* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.
| Ricardo Wurmus | 2016-02-24 | 1 | -0/+26 |
| * | gnu: Add r-org-hs-eg-db.•••* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
| Ricardo Wurmus | 2016-02-24 | 1 | -0/+26 |
| * | gnu: htseq: Add PySam to inputs.•••* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".
| Ricardo Wurmus | 2016-02-16 | 1 | -0/+2 |
| * | gnu: Add StringTie.•••* gnu/packages/bioinformatics.scm (stringtie): New variable.
| Ricardo Wurmus | 2016-02-16 | 1 | -0/+55 |
| * | gnu: prodigal: Update to 2.6.3.•••* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
| Ben Woodcroft | 2016-02-16 | 1 | -2/+2 |
| * | gnu: r-annotationdbi: Update to 1.32.3.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
| Ricardo Wurmus | 2016-02-15 | 1 | -2/+2 |
| * | 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.
| Ben Woodcroft | 2016-02-15 | 1 | -8/+19 |
| * | gnu: macs: Update to 2.1.0.20151222.•••* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
| Ricardo Wurmus | 2016-02-12 | 1 | -2/+2 |
| * | gnu: macs: Use "pypi-uri".•••* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to
build source URI.
| Ricardo Wurmus | 2016-02-12 | 1 | -3/+1 |
| * | gnu: Update sortmerna to 2.1.•••* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
| Ben J. Woodcroft | 2016-02-02 | 1 | -2/+2 |
| * | gnu: sra-tools: Update to 2.5.7.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
| Ben Woodcroft | 2016-01-26 | 1 | -2/+2 |
| * | gnu: ncbi-vdb: Update to 2.5.7.•••gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
| Ben Woodcroft | 2016-01-26 | 1 | -2/+2 |
| * | gnu: ngs-sdk: Update to 1.2.3.•••gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
| Ben Woodcroft | 2016-01-26 | 1 | -2/+2 |
| * | gnu: Add sortmerna.•••* gnu/packages/bioinformatics.scm (sortmerna): New variable.
| Ben Woodcroft | 2016-01-25 | 1 | -0/+43 |
| * | gnu: Add cufflinks.•••* gnu/packages/bioinformatics.scm (cufflinks): New variable.
| Ricardo Wurmus | 2016-01-23 | 1 | -0/+58 |
| * | 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.
| Ricardo Wurmus | 2016-01-23 | 1 | -0/+67 |
| * | 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".
| Ricardo Wurmus | 2016-01-23 | 1 | -8/+32 |
| * | gnu: star: Use "modify-phases" syntax.•••* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
syntax.
| Ricardo Wurmus | 2016-01-23 | 1 | -9/+9 |
| * | gnu: r-qtl: Update to 1.38-4.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
| Pjotr Prins | 2016-01-21 | 1 | -2/+2 |
| * | 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".
| Ricardo Wurmus | 2016-01-16 | 1 | -12/+15 |
| * | gnu: r-go-db: Add missing input.•••* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
"r-annotationdbi".
| Ricardo Wurmus | 2016-01-14 | 1 | -0/+2 |
| * | 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.
| Ricardo Wurmus | 2016-01-14 | 1 | -22/+16 |
| * | 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.
| Ben Woodcroft | 2016-01-14 | 1 | -3/+7 |
| * | 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.
| Ricardo Wurmus | 2016-01-13 | 1 | -27/+12 |
| * | gnu: Add fxtract.•••* gnu/packages/bioinformatics.scm (fxtract): New variable.
| Ben Woodcroft | 2016-01-12 | 1 | -0/+66 |
| * | 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.
| Ben Woodcroft | 2016-01-11 | 1 | -14/+3 |
| * | gnu: bedtools: Use modify-phases.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
| Ben Woodcroft | 2016-01-11 | 1 | -19/+19 |
| * | gnu: Add missing (gnu packages gcc) import.•••* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
| Mathieu Lirzin | 2016-01-08 | 1 | -0/+1 |
| * | gnu: Add genomation.•••* gnu/packages/bioinformatics.scm (r-genomation): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+43 |
| * | gnu: Add seqPattern.•••* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+26 |
| * | gnu: Add impute.•••* gnu/packages/bioinformatics.scm (r-impute): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+20 |
| * | gnu: Add BSgenome.•••* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+30 |
| * | gnu: Add topGO.•••* gnu/packages/bioinformatics.scm (r-topgo): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+29 |
| * | gnu: Add GO.db.•••* gnu/packages/bioinformatics.scm (r-go-db): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+20 |
| * | gnu: Add GenomicFeatures.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+41 |
| * | gnu: Add rtracklayer.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+45 |
| * | gnu: Add GenomicAlignments.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+33 |
| * | gnu: Add SummarizedExperiment.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+29 |
