~ruther/guix-local

ref: de585a7e644fdcb6ea05abde23f900d4242fcb48 guix-local/gnu/packages/bioinformatics.scm -rw-r--r-- 294.7 KiB
3dd50d97 — Ben Woodcroft 9 years ago 
gnu: vsearch: Update to 2.3.0.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.0.
99c90561 — Ben Woodcroft 9 years ago 
gnu: diamond: Update to 0.8.23.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.23.
9602e3cc — Ben Woodcroft 9 years ago 
gnu: python2-dendropy: Fix tests.

* gnu/packages/bioinformatics.scm (python2-dendropy)[source]: Use unpatched
source.
[arguments]: Use nose to run tests.
[native-inputs]: Add python2-nose.
fc47c7d6 — Ricardo Wurmus 9 years ago 
gnu: Add r-bsgenome-celegans-ucsc-ce10.

* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): New
variable.
2c3eb4b8 — Ben Woodcroft 9 years ago 
gnu: metabat: Update to 0.32.4-1.cbdca756.

* gnu/packages/bioinformatics.scm (metabat): Update to 0.32.4-1.cbdca756.
* gnu/packages/patches/metabat-remove-compilation-date.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
4bdc3df9 — Ben Woodcroft 9 years ago 
gnu: vsearch: Update to 2.1.2.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2.
2320e76b — Ricardo Wurmus 9 years ago 
gnu: sra-tools: Fix build on i686.

* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass
"VDB_LIBDIR" in make-flags; dynamically link libmagic.
99caa6f7 — Ben J Woodcroft 9 years ago 
gnu: python-plastid: Update to 1.4.6.

* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to
1.4.6.
[propagated-inputs]: Add python-termcolor.
f536dce5 — Marius Bakke 9 years ago 
gnu: python-pysam: Enable tests.

* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
dff26b23 — Marius Bakke 9 years ago 
gnu: python-pysam: Delete bundled htslib.

* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
397d463a — Marius Bakke 9 years ago 
gnu: python-pysam: Use 'modify-phases'.

* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.
bdc7be59 — Marius Bakke 9 years ago 
gnu: Add bcftools.

* gnu/packages/bioinformatics.scm (bcftools): New variable.
e301bfc8 — Marius Bakke 9 years ago 
gnu: python2-pbcore: Update to 1.2.10.

* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.
fd49eb21 — Marius Bakke 9 years ago 
gnu: python-pysam: Update to 0.9.1.4.

* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.
675d7ae2 — Ricardo Wurmus 9 years ago 
gnu: ncbi-vdb: Only build on i686 and x86_64.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.
af8de203 — Ben Woodcroft 9 years ago 
gnu: vsearch: Update to 2.1.1.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
f3cfe451 — Ricardo Wurmus 9 years ago 
gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene.

* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
  New variable.
684f29bd — Ricardo Wurmus 9 years ago 
gnu: Add r-grohmm.

* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
7f903d73 — Ricardo Wurmus 9 years ago 
gnu: Add r-systempiper.

* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
cb99d457 — Ricardo Wurmus 9 years ago 
gnu: Add r-shortread.

* gnu/packages/bioinformatics.scm (r-shortread): New variable.
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