| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: discrover: Comment on attempt of minimal texlive-union.•••* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal
texlive-union.
| Pierre Neidhardt | 2018-12-20 | 1 | -0/+16 |
| * | gnu: gess: Don't hardcode python version.•••* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
| Efraim Flashner | 2018-12-17 | 1 | -1/+4 |
| * | gnu: mash: Use C++ 14.•••I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore,
tweak the compilation to allow it to build with 0.7. The package also builds
with the current version of capnproto. I got the idea of changing the c++
version from here [1].
1: https://github.com/marbl/Mash/issues/98
* gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.
| Christopher Baines | 2018-12-05 | 1 | -0/+8 |
| * | gnu: pigx-rnaseq: Update to 0.0.5.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
| Ricardo Wurmus | 2018-12-04 | 1 | -3/+3 |
| * | gnu: bless: Adjust to zlib static output.•••* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC.
[arguments]: Adjust #:make-flags accordingly.
| Marius Bakke | 2018-11-24 | 1 | -1/+2 |
| * | gnu: mosaik: Fix FTBFS from b90289dadc8ee15848ce911a2bdcd3ae8302d58c.•••* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
| Marius Bakke | 2018-11-24 | 1 | -0/+1 |
| * | gnu: pigx-scrnaseq: Use latest snakemake.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
| Ricardo Wurmus | 2018-11-23 | 1 | -1/+1 |
| * | gnu: pigx-bsseq: Use latest snakemake.•••* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
| Ricardo Wurmus | 2018-11-23 | 1 | -1/+1 |
| * | gnu: pigx-chipseq: Use latest snakemake.•••* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
| Ricardo Wurmus | 2018-11-23 | 1 | -1/+1 |
| * | gnu: python-loompy: Remove python-typing.•••* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
| Ricardo Wurmus | 2018-11-23 | 1 | -2/+1 |
| * | Merge branch 'master' into core-updates | Marius Bakke | 2018-11-20 | 1 | -18/+93 |
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| | * | gnu: r-ensembldb: Update to 2.6.2.•••* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
| Roel Janssen | 2018-11-19 | 1 | -2/+2 |
| | * | gnu: r-msnbase: Update to 2.8.1.•••* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
| Roel Janssen | 2018-11-19 | 1 | -2/+2 |
| | * | gnu: r-genomeinfodb: Update to 1.18.1.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
| Roel Janssen | 2018-11-19 | 1 | -2/+2 |
| | * | gnu: Add nanopolish.•••* gnu/packages/bioinformatics.scm (nanopolish): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| pimi | 2018-11-15 | 1 | -0/+74 |
| | * | gnu: sambamba: Update to 0.6.8.•••* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
| Roel Janssen | 2018-11-15 | 1 | -12/+13 |
| * | | gnu: bioinformatics: Return #t from all phases and snippets.•••* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk)
(codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish)
(salmon): Return #t from all phases and snippets, use 'invoke' where
appropriate, and remove vestigal plumbing.
| Mark H Weaver | 2018-11-14 | 1 | -16/+31 |
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| * | gnu: Add jamm.•••* gnu/packages/bioinformatics.scm (jamm): New variable.
| Ricardo Wurmus | 2018-11-14 | 1 | -0/+79 |
| * | gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.•••* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-org-mm-eg-db: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-org-dm-eg-db: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-org-ce-eg-db: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-org-hs-eg-db: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-genomationdata: Update to 1.14.0.•••* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-go-db: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-genomeinfodbdata: Update to 1.2.0.•••* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
| Ricardo Wurmus | 2018-11-13 | 1 | -2/+2 |
| * | gnu: r-s4vectors: Update to 0.20.1.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
| Ricardo Wurmus | 2018-11-11 | 1 | -2/+2 |
| * | gnu: r-ensembldb: Update to 2.6.1.•••* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
| Ricardo Wurmus | 2018-11-09 | 1 | -2/+2 |
| * | gnu: r-biostrings: Update to 2.50.1.•••* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
| Ricardo Wurmus | 2018-11-09 | 1 | -2/+2 |
| * | gnu: r-biocviews: Update to 1.50.5.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
| Ricardo Wurmus | 2018-11-09 | 1 | -2/+2 |
| * | gnu: pplacer-scripts: Use INVOKE.•••* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -2/+1 |
| * | gnu: roary: Use INVOKE.•••* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -4/+5 |
| * | gnu: seek: Use INVOKE.•••* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
| Ricardo Wurmus | 2018-11-08 | 1 | -11/+14 |
| * | gnu: sailfish: Use INVOKE.•••* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
| Ricardo Wurmus | 2018-11-08 | 1 | -4/+4 |
| * | gnu: vsearch: Update to 2.9.1.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
| Ricardo Wurmus | 2018-11-08 | 1 | -2/+2 |
| * | gnu: sra-tools: Update to 2.9.3.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
| Ricardo Wurmus | 2018-11-08 | 1 | -14/+2 |
| * | gnu: plink-ng: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-08 | 1 | -5/+6 |
| * | gnu: ncbi-vdb: Update to 2.9.3.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
| Ricardo Wurmus | 2018-11-08 | 1 | -2/+2 |
| * | gnu: ngs-sdk: Update to 2.9.3.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
| Ricardo Wurmus | 2018-11-08 | 1 | -2/+2 |
| * | gnu: ngs-sdk: Use INVOKE.•••* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -3/+4 |
| * | gnu: emboss: Use INVOKE.•••* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -1/+1 |
| * | gnu: taxtastic: Use INVOKE.•••* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -2/+1 |
| * | gnu: sra-tools: Use INVOKE.•••* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -3/+3 |
| * | gnu: muscle: Use INVOKE.•••* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -2/+3 |
| * | gnu: newick-utils: Remove custom autoconf phase.•••* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
| Ricardo Wurmus | 2018-11-08 | 1 | -5/+0 |
| * | gnu: mash: Remove custom autoconf phase.•••* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
| Ricardo Wurmus | 2018-11-08 | 1 | -3/+1 |
| * | gnu: vsearch: Remove custom autogen phase.•••* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
| Ricardo Wurmus | 2018-11-08 | 1 | -5/+0 |
| * | gnu: java-picard-1.113: Use INVOKE.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -17/+19 |
| * | gnu: fraggenescan: Use INVOKE.•••* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
| Ricardo Wurmus | 2018-11-08 | 1 | -17/+22 |
| * | gnu: sailfish: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-08 | 1 | -6/+6 |
