| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
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* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
[source]: Remove bundled Cython sources in a snippet. Replace
".tar.gz" extension in file-name field with "-checkout".
[arguments]: Replace "enter-directory-and-clean-up" phase with
"enter-directory" phase, and add "patch-setuppy" phase.
[inputs]: Add python2-h5py. Move python2-cython ...
[native-inputs]: ... to this field.
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* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
CCFLAGS conditionally dependent on target system.
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* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
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* gnu/packages/bioinformatics.scm (mosaik): New variable.
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* gnu/packages/bioinformatics.scm (ngs-sdk): Correct typo.
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* gnu/packages/bioinformatics.scm (ngs-sdk)[supported-systems]: Keep only x86
based systems.
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* gnu/packages/bioinformatics.scm (diamond) [supported-systems]: Restrict to
x86_64-linux.
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* gnu/packages/bioinformatics.scm (bwa)[supported-systems]: Add field.
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* gnu/packages/bioinformatics.scm (vsearch)[supported-systems]: Restrict
to x86_64-linux.
Signed-off-by: Andreas Enge <andreas@enge.fr>
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* gnu/packages/bioinformatics.scm (clipper)[source]: Add file-name.
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* gnu/packages/bioinformatics.scm (vsearch): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
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* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
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* gnu/packages/bioinformatics.scm (seqmagick): New variable.
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* gnu/packages/bioinformatics.scm (r-qtl): New variable.
Co-authored-by: Pjotr Prins <pjotr.guix@thebird.nl>
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* gnu/packages/bioinformatics.scm (bioruby): New variable.
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* gnu/packages/bioinformatics.scm (mafft): New variable.
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* gnu/packages/bioinformatics.scm (bio-locus): New variable.
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This reverts commit b429c4fbb06299ce10ecc113a7818bf777c63a6e.
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* gnu/packages/bioinformatics.scm (bio-locus): New variable.
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* gnu/packages/bioinformatics.scm (deeptools): New variable.
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* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
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* gnu/packages/bioinformatics.scm (shogun): Move from here...
* gnu/packages/machine-learning.scm (shogun): ...to here.
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* gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
* gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.
* gnu-system.am (dist_patch_DATA): Register patch.
Signed-off-by: Andreas Enge <andreas@enge.fr>
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* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
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* gnu/packages/bioinformatics.scm (aragorn): New variable.
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* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in
'fix-includes' phase.
[license]: Fix misspelling.
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* gnu/packages/bioinformatics.scm (metabat): New variable.
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* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase
"use-samtools-headers" after "enter-dir" phase.
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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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