| Age | Commit message (Expand) | Author |
|---|
| 2015-05-05 | gnu: vcftools: Remove "-m64" from CFLAGS.•••* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to
remove "-m64" flag.
| Ricardo Wurmus |
| 2015-05-04 | 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.
| Ricardo Wurmus |
| 2015-05-04 | gnu: Add samtools-0.1.19.•••* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
| Ricardo Wurmus |
| 2015-05-04 | gnu: samtools: Install libbam.a library.•••* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-library" to install the libbam.a library.
| Ricardo Wurmus |
| 2015-05-04 | gnu: samtools: Remove patch-makefile-curses phase.•••* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
patch-makefile-curses phase, use make-flags instead.
| Ricardo Wurmus |
| 2015-04-27 | gnu: flexbar: Enable tests.•••* gnu/packages/bioinformatics.scm (flexbar): Enable tests.
| Ricardo Wurmus |
| 2015-04-21 | gnu: Add eXpress.•••* gnu/packages/bioinformatics.scm (express): New variable.
| Ricardo Wurmus |
| 2015-04-21 | gnu: Add bamtools.•••* gnu/packages/bioinformatics.scm (bamtools): New variable.
| Ricardo Wurmus |
| 2015-04-21 | gnu: Add subread.•••* gnu/packages/bioinformatics.scm (subread): New variable.
| Ricardo Wurmus |
| 2015-04-20 | gnu: Add sra-tools.•••* gnu/packages/bioinformatics.scm (sra-tools): New variable.
| Ricardo Wurmus |
| 2015-04-20 | gnu: Add NCBI VDB.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
| Ricardo Wurmus |
| 2015-04-20 | gnu: Add NGS Java bindings.•••* gnu/packages/bioinformatics.scm (ngs-java): New variable.
| Ricardo Wurmus |
| 2015-04-20 | gnu: Add NGS SDK.•••* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
| Ricardo Wurmus |
| 2015-04-20 | gnu: Add Biopython.•••* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
variables.
| Ricardo Wurmus |
| 2015-04-16 | gnu: Add FASTX Toolkit.•••* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
| Ricardo Wurmus |
| 2015-04-13 | gnu: rseqc: Update hash.•••* gnu/packages/bioinformatics.scm (rseqc): Update hash.
| Ricardo Wurmus |
| 2015-04-10 | gnu: Add GRIT.•••* gnu/packages/bioinformatics.scm (grit): New variable.
| Ricardo Wurmus |
| 2015-04-09 | gnu: Add Shogun.•••* gnu/packages/bioinformatics.scm (shogun): New variable.
| Ricardo Wurmus |
| 2015-04-01 | gnu: Add clustal omega.•••* gnu/packages/bioinformatics.scm (clustal-omega): New variable.
| Ricardo Wurmus |
| 2015-03-31 | gnu: pbtranscript-tofu: Add missing inputs.•••* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
runtime inputs.
| Ricardo Wurmus |
| 2015-03-31 | gnu: pbtranscript-tofu: Delete pre-built libraries.•••* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
"build" directory and any shared objects after unpacking.
| Ricardo Wurmus |
| 2015-03-31 | gnu: Add vcftools.•••* gnu/packages/bioinformatics.scm (vcftools): New variable.
| Ricardo Wurmus |
| 2015-03-31 | gnu: Add cutadapt.•••* gnu/packages/bioinformatics.scm (cutadapt): New variable.
| Ricardo Wurmus |
| 2015-03-24 | gnu: Add pbtranscript-tofu.•••* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
| Ricardo Wurmus |
| 2015-03-24 | gnu: Add python2-bx-python.•••* gnu/packages/bioinformatics.scm (python2-bx-python): New variable.
| Ricardo Wurmus |
| 2015-03-24 | gnu: Add python2-pbcore.•••* gnu/packages/bioinformatics.scm (python2-pbcore): New variable.
| Ricardo Wurmus |
| 2015-03-17 | gnu: Add MISO.•••* gnu/packages/bioinformatics.scm (miso): New variable.
| Ricardo Wurmus |
| 2015-03-17 | gnu: Add bwa.•••* gnu/packages/bioinformatics.scm (bwa): New variable.
| Ricardo Wurmus |
| 2015-03-10 | gnu: Add htsjdk.•••* gnu/packages/bioinformatics.scm (htsjdk): New variable.
| Ricardo Wurmus |
| 2015-03-04 | Merge branch 'core-updates'. | Ludovic Courtès |
| 2015-03-02 | gnu: Add crossmap.•••* 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.
| Ricardo Wurmus |
| 2015-03-02 | gnu: Add CLIPper.•••* gnu/packages/bioinformatics.scm (clipper): New variable.
| Ricardo Wurmus |
| 2015-03-02 | gnu: Add MACS.•••* gnu/packages/bioinformatics.scm (macs): New variable.
| Ricardo Wurmus |
| 2015-03-02 | gnu: Add pybedtools.•••* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
| Ricardo Wurmus |
| 2015-02-28 | gnu: Add 'file-name' fields for github source tarballs without a name.•••* 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.
| Mark H Weaver |
| 2015-02-27 | gnu: Remove now unneeded 'unpack' phases for unzip.•••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.
| Ludovic Courtès |
| 2015-02-20 | gnu: Add HTSeq.•••* gnu/packages/bioinformatics.scm (htseq): New variable.
| Ricardo Wurmus |
| 2015-02-19 | gnu: Add RSeQC.•••* gnu/packages/bioinformatics.scm (rseqc): New variable.
| Ricardo Wurmus |
| 2015-02-13 | gnu: Add bedops.•••* gnu/packages/bioinformatics.scm (bedops): New variable.
| Ricardo Wurmus |
| 2015-02-12 | gnu: hisat: fix build on non-x86_64.•••* gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to
make-flags on architectures other than x86_64.
| Ricardo Wurmus |
| 2015-02-10 | gnu: Add STAR.•••* gnu/packages/bioinformatics.scm (star): New variable.
| Ricardo Wurmus |
| 2015-02-10 | gnu: Add HISAT.•••* gnu/packages/bioinformatics.scm (hisat): New variable.
| Ricardo Wurmus |
| 2015-02-09 | gnu: Add flexbar.•••* gnu/packages/bioinformatics.scm (flexbar): New variable.
| Ricardo Wurmus |
| 2015-02-09 | gnu: Add seqan.•••* gnu/packages/bioinformatics.scm (seqan): New variable.
| Ricardo Wurmus |
| 2015-01-30 | gnu: bowtie: fix build errors•••* 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.
| Ricardo Wurmus |
| 2014-12-19 | gnu: Add bowtie•••* gnu/packages/bioinformatics.scm (bowtie): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Ricardo Wurmus |
| 2014-12-16 | gnu: Add bedtools•••* gnu/packages/bioinformatics.scm (bedtools): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Ricardo Wurmus |
| 2014-12-16 | gnu: samtools: disable tests for non-64-bit systems•••* 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>
| Ricardo Wurmus |
| 2014-12-13 | gnu: Add samtools•••* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Ricardo Wurmus |
