| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.
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* gnu/packages/bioinformatics.scm (codingquarry): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use
ant-build-system.
[arguments]: Adapt for ant-build-system.
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* gnu/packages/bioinformatics.scm (pyicoteo): New variable.
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* gnu/packages/bioinformatics.scm (bioawk): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move
"python-cython" and "python-setuptools" from here...
[native-inputs]: ... to here.
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* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
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* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
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* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
New variables.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
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* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
...here.
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* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
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* gnu/packages/bioinformatics.scm (pepr): New variable.
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* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
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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).
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This is a followup to 1baee94.
* gnu/packages/bioinformatics.scm: Add missing import.
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* gnu/packages/bioinformatics.scm (libbigwig): New variable.
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* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add
"r-graph".
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* gnu/packages/bioinformatics.scm (r-graph): New variable.
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* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable.
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* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.
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* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.
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* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
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* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".
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* gnu/packages/bioinformatics.scm (stringtie): New variable.
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* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0.
[origin]: Adapt to changes in bundling of cityhash.
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* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
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* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to
build source URI.
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* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
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* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
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gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
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gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
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* gnu/packages/bioinformatics.scm (sortmerna): New variable.
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* gnu/packages/bioinformatics.scm (cufflinks): New variable.
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* 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.
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* 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".
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* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
syntax.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
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* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
"LIBCURSES" make flag; delete "configure" phase; disable tests outside
of "substitute-keyword-arguments".
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* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
"r-annotationdbi".
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* 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.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
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* 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.
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* gnu/packages/bioinformatics.scm (fxtract): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
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