Age | Commit message (Collapse) | Author |
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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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* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
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* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
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* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
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* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
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* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
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* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
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