~ruther/guix-local

ref: 1cd5f1776da210b1d2dc0594de3597881d0e0231 guix-local/gnu/packages/bioinformatics.scm -rw-r--r-- 388.4 KiB
09ec5a0f — Mark H Weaver 8 years ago 
Merge branch 'master' into core-updates
96348048 — Ricardo Wurmus 8 years ago 
gnu: Add bismark.

* gnu/packages/bioinformatics.scm (bismark): New variable.
86763fdd — Ricardo Wurmus 8 years ago 
gnu: Add r-dexseq.

* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
cc294bce — Mark H Weaver 8 years ago 
Merge branch 'master' into core-updates
1b22ecda — Ricardo Wurmus 8 years ago 
gnu: r-wgcna: Update to 1.61.

* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61.
[propagated-inputs]: Add r-rcpp, r-robust, r-survival.
18f5d2a7 — Ricardo Wurmus 8 years ago 
gnu: Add reference to (gnu packages graph).

This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3.
2d9495da — Mark H Weaver 8 years ago 
Merge branch 'master' into core-updates
9d217d27 — Tobias Geerinckx-Rice 8 years ago 
gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Restore hash from before the tarball changed in place.  It changed back.

This reverts commit fd4085793818ab2aea28dfeeb2728f6f02416c4c.
f167595b — Mark H Weaver 8 years ago 
Merge branch 'master' into core-updates
a56bf101 — Ludovic Courtès 8 years ago 
gnu: perl: Work around more "dotless @INC" build issues.

* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path'
phase.
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment
'configure' phase to set PERL5LIB.
* gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument.
7cb61550 — Efraim Flashner 8 years ago 
gnu: bioinformatics.scm: Use (gnu packages cran) module.

This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249.

* gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
5e0de298 — Ricardo Wurmus 8 years ago 
gnu: r-seqminer: Update to 6.0.

* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
4e0c847d — Ricardo Wurmus 8 years ago 
gnu: r-wgcna: Update to 1.60.

* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
c8a9b2bc — Ricardo Wurmus 8 years ago 
gnu: r-qtl: Update to 1.41-6.

* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
023aa8ff — Ricardo Wurmus 8 years ago 
gnu: r-seqinr: Update to 3.4-5.

* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
7150f1c3 — Ricardo Wurmus 8 years ago 
gnu: r-optparse: Update to 1.4.4.

* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
3f6ec083 — Ricardo Wurmus 8 years ago 
gnu: r-bookdown: Update to 0.4.

* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
75e6639f — Ben Woodcroft 8 years ago 
gnu: htseq: Use PyPI URI.

This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf.

* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
92971d68 — Ben Woodcroft 8 years ago 
gnu: htseq: Update to 0.9.1.

* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package.  Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
f1915a5d — Roel Janssen 8 years ago 
gnu: r-deseq2: Update to 1.16.1.

* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
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