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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 (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/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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* gnu/packages/bioinformatics.scm (hisat): New variable.
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* gnu/packages/bioinformatics.scm (flexbar): New variable.
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* gnu/packages/bioinformatics.scm (seqan): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (bowtie): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/bioinformatics.scm (bedtools): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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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>
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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>
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