| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
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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.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
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* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC.
[arguments]: Adjust #:make-flags accordingly.
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* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
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* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
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* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (nanopolish): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
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* 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.
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* gnu/packages/bioinformatics.scm (jamm): New variable.
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* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
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* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
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* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
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* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
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* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
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* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
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* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
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* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
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* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
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* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
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* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
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* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
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* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
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* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
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* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
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* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
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* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
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* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
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* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
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* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
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* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
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* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
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* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
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* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
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