~ruther/guix-local

ref: 7b158c4ee2d4b5cf6a2cd9bf0246465c3c8a06ca guix-local/gnu/packages/bioinformatics.scm -rw-r--r-- 162.2 KiB
afe9f409 — Mark H Weaver 10 years ago 
Merge branch 'master' into core-updates
2309ed68 — Ricardo Wurmus 10 years ago 
gnu: samtools-0.1: Adapt to changes in "samtools" variable.

* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
  "LIBCURSES" make flag; delete "configure" phase; disable tests outside
  of "substitute-keyword-arguments".
3141b83d — Ricardo Wurmus 10 years ago 
gnu: r-go-db: Add missing input.

* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
  "r-annotationdbi".
0047d26a — Ricardo Wurmus 10 years ago 
gnu: bowtie: Update to 2.2.6.

* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
6b6f7d6a — Ben Woodcroft 10 years ago 
gnu: orfm: Update to 0.5.3.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
8c986ab1 — Ludovic Courtès 10 years ago 
Merge branch 'master' into core-updates
c4473411 — Ricardo Wurmus 10 years ago 
gnu: samtools: Update to 1.3.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
81f3e0c1 — Ben Woodcroft 10 years ago 
gnu: Add fxtract.

* gnu/packages/bioinformatics.scm (fxtract): New variable.
9b9b7ffd — Ben Woodcroft 10 years ago 
gnu: bedtools: Update to 2.25.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'.  Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
6573ac82 — Ben Woodcroft 10 years ago 
gnu: bedtools: Use modify-phases.

* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2409f37f — Mathieu Lirzin 10 years ago 
gnu: Add missing (gnu packages gcc) import.

* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
cb933df6 — Ricardo Wurmus 10 years ago 
gnu: Add genomation.

* gnu/packages/bioinformatics.scm (r-genomation): New variable.
03ea5a35 — Ricardo Wurmus 10 years ago 
gnu: Add seqPattern.

* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
c43a011d — Ricardo Wurmus 10 years ago 
gnu: Add impute.

* gnu/packages/bioinformatics.scm (r-impute): New variable.
c63cef66 — Ricardo Wurmus 10 years ago 
gnu: Add BSgenome.

* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
d547ce5e — Ricardo Wurmus 10 years ago 
gnu: Add topGO.

* gnu/packages/bioinformatics.scm (r-topgo): New variable.
fb25d880 — Ricardo Wurmus 10 years ago 
gnu: Add GO.db.

* gnu/packages/bioinformatics.scm (r-go-db): New variable.
2fd7c049 — Ricardo Wurmus 10 years ago 
gnu: Add GenomicFeatures.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
317755ff — Ricardo Wurmus 10 years ago 
gnu: Add rtracklayer.

* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
d8a828af — Ricardo Wurmus 10 years ago 
gnu: Add GenomicAlignments.

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