~ruther/guix-local: gnu/packages/bioinformatics.scm bfa0d1e77351ee0be85c06595e6eb398731adde2

bfa0d1e7 — Roel Janssen 8 years ago

gnu: r-sva: Update to 3.24.4.

* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.

d931a4bb — Efraim Flashner 8 years ago

gnu: metabat: Limit to x86_64 and i686 only.

* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.

a9085f0c — Ben Woodcroft 8 years ago

gnu: metabat: Update to 2.11.2.

* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.

f3f68a44 — Ben Woodcroft 9 years ago

gnu: metabat: Update to 2.11.1.

* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

897ab082 — Ben Woodcroft 9 years ago

gnu: python-plastid: Update to 0.4.8.

* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.

0620387a — Ben Woodcroft 8 years ago

gnu: bcftools: Update to 1.5.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag.  Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

63fa0ffc — Ben Woodcroft 9 years ago

gnu: samtools: Update to 1.5.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.

4fb6d128 — Ben Woodcroft 9 years ago

gnu: htslib: Update to 1.5.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.

60739965 — Ben Woodcroft 9 years ago

gnu: python-pysam: Update to 0.11.2.2.

* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.

bca2c576 — Ben Woodcroft 9 years ago

gnu: bamm: Use htslib-1.3.

* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.

98593f9f — Ben Woodcroft 9 years ago

gnu: bcftools: Update to 1.4.1.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch.  Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

4ab16440 — Ben Woodcroft 9 years ago

gnu: samtools: Update to 1.4.1.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.

a9e4a1e6 — Ben Woodcroft 9 years ago

gnu: htslib: Update to 1.4.1.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.

c842d425 — Ben Woodcroft 9 years ago

gnu: samtools: Use "modify-phases" syntax.

* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.

3a4b0b12 — Ricardo Wurmus 8 years ago

gnu: r-s4vectors: Update to 0.14.3.

* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.

a35a1e9c — Ricardo Wurmus 8 years ago

gnu: r-genomicranges: Update to 1.28.4.

* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.

fd408579 — Ricardo Wurmus 9 years ago

gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Update hash because the tarball changed in place.

2324541b — Efraim Flashner 9 years ago

gnu: sortmerna: Limit support to x86_64 and i686 only.

* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.

2805f9b2 — Efraim Flashner 9 years ago

gnu: raxml: Limit to x86_64 and i686 only.

* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.

06e37236 — Ben Woodcroft 9 years ago

gnu: bowtie: Use 'modify-phases'.

* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.