| Age | Commit message (Expand) | Author |
|---|
| 2015-07-09 | gnu: preseq: Move "use-samtools-headers" phase.•••* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase
"use-samtools-headers" after "enter-dir" phase.
| Ricardo Wurmus |
| 2015-07-08 | gnu: Add preseq.•••* gnu/packages/bioinformatics.scm (preseq): New variable.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add them.
| Ricardo Wurmus |
| 2015-07-08 | gnu: samtools: Install headers.•••* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-headers" to install header files.
| Ricardo Wurmus |
| 2015-07-07 | gnu: samtools: Update to 1.2.•••* gnu/packages/bioinformatics.scm (samtools): Update to 1.2.
| Ricardo Wurmus |
| 2015-07-05 | gnu: Add prodigal.•••* gnu/packages/bioinformatics.scm (prodigal): New variable.
| Ben Woodcroft |
| 2015-07-04 | gnu: shogun: Build with install RPATH.•••* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to
build with install RPATH.
| Ricardo Wurmus |
| 2015-07-02 | gnu: Add WarpedLMM.•••* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
| Ricardo Wurmus |
| 2015-06-29 | gnu: Add Blast+.•••* gnu/packages/bioinformatics.scm (blast+): New variable.
| Ricardo Wurmus |
| 2015-06-29 | gnu: Add plink.•••* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
| Ricardo Wurmus |
| 2015-06-24 | gnu: Add hmmer.•••* gnu/packages/bioinformatics.scm (hmmer): New variable.
| Ben Woodcroft |
| 2015-06-23 | gnu: star: Update to 2.4.2a.•••* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.
| Ricardo Wurmus |
| 2015-06-23 | gnu: miso: Install executables.•••* gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use
"setuptools" so that executables are built.
* gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock"
and "python2-pytz".
| Ricardo Wurmus |
| 2015-06-23 | gnu: Add idr.•••* gnu/packages/bioinformatics.scm (idr): New variable.
| Ricardo Wurmus |
| 2015-06-21 | gnu: Add fasttree.•••* gnu/packages/bioinformatics.scm (fasttree): New variable.
| Ben Woodcroft |
| 2015-06-17 | gnu: Add diamond.•••* gnu/packages/bioinformatics.scm (diamond): New variable.
| Ben Woodcroft |
| 2015-06-17 | gnu: miso: Use HTTPS URL.•••* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
downloading the source tarball.
| Ricardo Wurmus |
| 2015-06-17 | gnu: bedops: Update to 2.4.14.•••* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
| Ricardo Wurmus |
| 2015-06-15 | gnu: orfm: Update to 0.4.1.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
| Ricardo Wurmus |
| 2015-06-12 | gnu: Add OrfM.•••* gnu/packages/bioinformatics.scm (orfm): New variable.
Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
| Ben Woodcroft |
| 2015-06-12 | gnu: Add Couger.•••* gnu/packages/bioinformatics.scm (couger): New variable.
| Ricardo Wurmus |
| 2015-06-12 | gnu: ngs-sdk: Update to version 1.1.1.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
| Ricardo Wurmus |
| 2015-06-02 | gnu: Add HTSlib.•••* gnu/packages/bioinformatics.scm (htslib): New variable.
| Ricardo Wurmus |
| 2015-06-02 | gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
"linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
i686.
| Ricardo Wurmus |
| 2015-05-27 | gnu: Add edirect.•••* gnu/packages/bioinformatics.scm (edirect): New variable.
| Ricardo Wurmus |
| 2015-05-27 | gnu: shogun: Remove non-free source files.•••* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove
non-free sources.
| Ricardo Wurmus |
| 2015-05-22 | gnu: Add rsem.•••* gnu/packages/bioinformatics.scm (rsem): New variable.
* gnu/packages/patches/rsem-makefile.patch: New file.
| Ricardo Wurmus |
| 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 |
