| Commit message (Collapse) | Author | Age |
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* 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.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-headers" to install header files.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.2.
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* gnu/packages/bioinformatics.scm (prodigal): New variable.
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* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to
build with install RPATH.
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* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
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* gnu/packages/bioinformatics.scm (blast+): New variable.
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* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
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* gnu/packages/bioinformatics.scm (hmmer): New variable.
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* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.
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* 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".
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* gnu/packages/bioinformatics.scm (idr): New variable.
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* gnu/packages/bioinformatics.scm (fasttree): New variable.
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* gnu/packages/bioinformatics.scm (diamond): New variable.
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* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
downloading the source tarball.
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* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
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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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