~ruther/guix-local

ref: d7786ce9b052dd6716aac1ec63cee9951eaa65a7 guix-local/gnu/packages/bioinformatics.scm -rw-r--r-- 162.0 KiB
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.
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.
6e76dda2 — Ricardo Wurmus 10 years ago 
gnu: Add SummarizedExperiment.

* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
f8d74f70 — Ricardo Wurmus 10 years ago 
gnu: Add Rsamtools.

* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
bf159353 — Ricardo Wurmus 10 years ago 
gnu: Add Biostrings.

* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
e91d362e — Ricardo Wurmus 10 years ago 
gnu: Add BiocParallel.

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