~ruther/guix-local

ref: 85960693e4eec79a3cae1db4dc5ff47a1d2703e6 guix-local/gnu/packages/bioinformatics.scm -rw-r--r-- 170.3 KiB
ce294c04 — Ben J. Woodcroft 10 years ago 
gnu: Update sortmerna to 2.1.

* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
a78d62f4 — Ben Woodcroft 10 years ago 
gnu: sra-tools: Update to 2.5.7.

* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
fe91666b — Ben Woodcroft 10 years ago 
gnu: ncbi-vdb: Update to 2.5.7.

gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
d3b39bc2 — Ben Woodcroft 10 years ago 
gnu: ngs-sdk: Update to 1.2.3.

gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
412bee5e — Mark H Weaver 10 years ago 
Merge branch 'master' into core-updates
bcadaf00 — Ben Woodcroft 10 years ago 
gnu: Add sortmerna.

* gnu/packages/bioinformatics.scm (sortmerna): New variable.
3a40a92c — Ricardo Wurmus 10 years ago 
gnu: Add cufflinks.

* gnu/packages/bioinformatics.scm (cufflinks): New variable.
94ce537e — Ricardo Wurmus 10 years ago 
gnu: Add TopHat.

* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
3062d750 — Ricardo Wurmus 10 years ago 
gnu: star: Update to 2.5.1b.

* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
c0266e8d — Ricardo Wurmus 10 years ago 
gnu: star: Use "modify-phases" syntax.

* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
  syntax.
89709287 — Pjotr Prins 10 years ago 
gnu: r-qtl: Update to 1.38-4.

* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
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.
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