| Age | Commit message (Expand) | Author |
|---|
| 2015-11-20 | gnu: preseq: Update to 2.0....* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
file.
* gnu-system.am (dist_patch_DATA): Remove them.
| Ricardo Wurmus |
| 2015-11-20 | gnu: Add smithlab-cpp....* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
| Ricardo Wurmus |
| 2015-11-20 | gnu: edirect: Update home page....* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
slash to home page.
| Ricardo Wurmus |
| 2015-11-20 | gnu: sra-tools: Update to 2.5.4....* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
| Ricardo Wurmus |
| 2015-11-20 | gnu: ncbi-vdb: Update to 2.5.4....* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
| Ricardo Wurmus |
| 2015-11-20 | gnu: ngs-java: Update to 1.2.2....* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".
| Ricardo Wurmus |
| 2015-11-20 | gnu: ngs-sdk: Update to 1.2.2....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
| Ricardo Wurmus |
| 2015-11-20 | gnu: bless: Build only for x86_64....* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
| Ricardo Wurmus |
| 2015-11-20 | gnu: htseq: Propagate numpy....* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
from here ...
[propagated-inputs]: ... to here.
| Ricardo Wurmus |
| 2015-11-12 | gnu: mosaik: Build only on x86_64....* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add
field.
| Ricardo Wurmus |
| 2015-11-06 | gnu: bless: Correct indentation and home-page....* gnu/packages/bioinformatics.scm (bless): Fix indentation.
[home-page]: Replace broken URL.
| Ricardo Wurmus |
| 2015-11-06 | gnu: Add BLESS....* gnu/packages/bioinformatics.scm (bless): New variable.
Co-authored-by: Diane Trout <diane@ghic.org>
| Ricardo Wurmus |
| 2015-11-02 | gnu: hisat: Disable build on non-x86_64....* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
| Ricardo Wurmus |
| 2015-11-02 | gnu: Add express-beta-diversity....* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Ben Woodcroft |
| 2015-10-28 | gnu: pbtranscript-tofu: Update to 2.2.3....* 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.
| Ricardo Wurmus |
| 2015-10-27 | gnu: subread: Use SSE optimizations on x86_64 only....* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
CCFLAGS conditionally dependent on target system.
| Ricardo Wurmus |
| 2015-10-27 | gnu: crossmap: Update to 0.2.1....* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
| Ricardo Wurmus |
| 2015-10-22 | gnu: Add MOSAIK....* gnu/packages/bioinformatics.scm (mosaik): New variable.
| Ricardo Wurmus |
| 2015-10-17 | gnu: ngs-sdk: Correct typo....* gnu/packages/bioinformatics.scm (ngs-sdk): Correct typo.
| Andreas Enge |
| 2015-10-17 | gnu: ngs-sdk: Remove unsupported systems....* gnu/packages/bioinformatics.scm (ngs-sdk)[supported-systems]: Keep only x86
based systems.
| Andreas Enge |
| 2015-10-14 | gnu: diamond: Restrict supported systems to x86_64-linux....* gnu/packages/bioinformatics.scm (diamond) [supported-systems]: Restrict to
x86_64-linux.
| Ben Woodcroft |
| 2015-10-12 | gnu: bwa: Disable on non-x86_64....* gnu/packages/bioinformatics.scm (bwa)[supported-systems]: Add field.
| Ricardo Wurmus |
| 2015-10-03 | gnu: vsearch: Restrict supported systems to x86_64-linux....* gnu/packages/bioinformatics.scm (vsearch)[supported-systems]: Restrict
to x86_64-linux.
Signed-off-by: Andreas Enge <andreas@enge.fr>
| Ben Woodcroft |
| 2015-10-02 | gnu: clipper: Add 'file-name' field to source origin....* gnu/packages/bioinformatics.scm (clipper)[source]: Add file-name.
| Mark H Weaver |
| 2015-10-01 | gnu: Add vsearch....* gnu/packages/bioinformatics.scm (vsearch): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Ben Woodcroft |
| 2015-09-28 | gnu: Add bio-blastxmlparser....* gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
| Pjotr Prins |
| 2015-09-26 | Merge branch 'core-updates' | Ludovic Courtès |
| 2015-09-25 | gnu: Add seqmagick....* gnu/packages/bioinformatics.scm (seqmagick): New variable.
| Ben Woodcroft |
| 2015-09-22 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2015-09-20 | gnu: Add R/qtl....* gnu/packages/bioinformatics.scm (r-qtl): New variable.
Co-authored-by: Pjotr Prins <pjotr.guix@thebird.nl>
| Andreas Enge |
| 2015-09-19 | gnu: Add bioruby....* gnu/packages/bioinformatics.scm (bioruby): New variable.
| Pjotr Prins |
| 2015-09-16 | gnu: Add mafft....* gnu/packages/bioinformatics.scm (mafft): New variable.
| Ben Woodcroft |
| 2015-09-14 | gnu: Add bio-locus....* gnu/packages/bioinformatics.scm (bio-locus): New variable.
| Pjotr Prins |
| 2015-09-14 | Revert "gnu: Add bio-locus."...This reverts commit b429c4fbb06299ce10ecc113a7818bf777c63a6e.
| David Thompson |
| 2015-09-14 | gnu: Add bio-locus....* gnu/packages/bioinformatics.scm (bio-locus): New variable.
| Pjotr Prins |
| 2015-09-13 | Merge branch 'master' into core-updates | Ludovic Courtès |
| 2015-09-02 | gnu: Add deeptools....* gnu/packages/bioinformatics.scm (deeptools): New variable.
| Ricardo Wurmus |
| 2015-08-29 | gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases....* 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.
| Ludovic Courtès |
| 2015-08-26 | gnu: Add BioPerl....* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
| Ricardo Wurmus |
| 2015-08-14 | gnu: shogun: Move package to machine-learning.scm....* gnu/packages/bioinformatics.scm (shogun): Move from here...
* gnu/packages/machine-learning.scm (shogun): ...to here.
| Ricardo Wurmus |
| 2015-07-25 | gnu: bedtools: Add patch to fix compilation on 32 bit systems....* 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>
| Ben Woodcroft |
| 2015-07-25 | gnu: bedtools: Update to 2.24.0....* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
| Ben Woodcroft |
| 2015-07-21 | gnu: Add aragorn....* gnu/packages/bioinformatics.scm (aragorn): New variable.
| Ben Woodcroft |
| 2015-07-19 | gnu: metabat: Minor tweaks....* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in
'fix-includes' phase.
[license]: Fix misspelling.
| Mark H Weaver |
| 2015-07-19 | gnu: Add metabat....* gnu/packages/bioinformatics.scm (metabat): New variable.
| Ben Woodcroft |
| 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 |
