Age | Commit message (Collapse) | Author |
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
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* gnu/packages/bioinformatics.scm (orfm): New variable.
Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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* gnu/packages/bioinformatics.scm (couger): New variable.
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* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
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* gnu/packages/bioinformatics.scm (htslib): New variable.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
"linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
i686.
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* gnu/packages/bioinformatics.scm (edirect): New variable.
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* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove
non-free sources.
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* gnu/packages/bioinformatics.scm (rsem): New variable.
* gnu/packages/patches/rsem-makefile.patch: New file.
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* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to
remove "-m64" flag.
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* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase
setting $LDFLAGS to set the rpath to $out/lib/bamtools.
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* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-library" to install the libbam.a library.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
patch-makefile-curses phase, use make-flags instead.
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* gnu/packages/bioinformatics.scm (flexbar): Enable tests.
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* gnu/packages/bioinformatics.scm (express): New variable.
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* gnu/packages/bioinformatics.scm (bamtools): New variable.
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* gnu/packages/bioinformatics.scm (subread): New variable.
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* gnu/packages/bioinformatics.scm (sra-tools): New variable.
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* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
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* gnu/packages/bioinformatics.scm (ngs-java): New variable.
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* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
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* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
variables.
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* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
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* gnu/packages/bioinformatics.scm (rseqc): Update hash.
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* gnu/packages/bioinformatics.scm (grit): New variable.
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* gnu/packages/bioinformatics.scm (shogun): New variable.
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* gnu/packages/bioinformatics.scm (clustal-omega): New variable.
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
runtime inputs.
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
"build" directory and any shared objects after unpacking.
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* gnu/packages/bioinformatics.scm (vcftools): New variable.
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* gnu/packages/bioinformatics.scm (cutadapt): New variable.
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
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* gnu/packages/bioinformatics.scm (python2-bx-python): New variable.
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* gnu/packages/bioinformatics.scm (python2-pbcore): New variable.
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* gnu/packages/bioinformatics.scm (miso): New variable.
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* gnu/packages/bioinformatics.scm (bwa): New variable.
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* gnu/packages/bioinformatics.scm (htsjdk): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (clipper): New variable.
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* gnu/packages/bioinformatics.scm (macs): New variable.
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* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
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* 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.
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This is a followup to commit cd0385b.
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove 'unpack'
phase.
* gnu/packages/image.scm (freeimage): Likewise.
* gnu/packages/python.scm (python2-cssutils): Likewise.
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* gnu/packages/bioinformatics.scm (htseq): New variable.
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* gnu/packages/bioinformatics.scm (rseqc): New variable.
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* gnu/packages/bioinformatics.scm (bedops): New variable.
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* gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to
make-flags on architectures other than x86_64.
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* gnu/packages/bioinformatics.scm (star): New variable.
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