aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
AgeCommit message (Collapse)Author
2018-11-14gnu: bioinformatics: Return #t from all phases and snippets.Mark H Weaver
* 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.
2018-11-14gnu: Add jamm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-13gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4.
2018-11-13gnu: r-org-mm-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-dm-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-ce-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-hs-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13gnu: r-genomationdata: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13gnu: r-go-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13gnu: r-genomeinfodbdata: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-11gnu: r-s4vectors: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-09gnu: r-ensembldb: Update to 2.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
2018-11-09gnu: r-biostrings: Update to 2.50.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
2018-11-09gnu: r-biocviews: Update to 1.50.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
2018-11-08gnu: pplacer-scripts: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: roary: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: seek: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
2018-11-08gnu: sailfish: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of SYSTEM*.
2018-11-08gnu: vsearch: Update to 2.9.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1. * gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
2018-11-08gnu: sra-tools: Update to 2.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3. [arguments]: Remove build phase patch-away-glibc-conflict.
2018-11-08gnu: plink-ng: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
2018-11-08gnu: ncbi-vdb: Update to 2.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
2018-11-08gnu: ngs-sdk: Update to 2.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
2018-11-08gnu: ngs-sdk: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: emboss: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: taxtastic: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: sra-tools: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: muscle: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: newick-utils: Remove custom autoconf phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08gnu: mash: Remove custom autoconf phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08gnu: vsearch: Remove custom autogen phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08gnu: java-picard-1.113: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: fraggenescan: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in build phases and return #T unconditionally.
2018-11-08gnu: sailfish: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08gnu: ngs-sdk: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
2018-11-08gnu: ncbi-vdb: Use INVOKE and end phases on #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and unconditionally end phases with #T.
2018-11-08gnu: ncbi-vdb: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git. [arguments]: Add phase to make checkout writable.
2018-11-08gnu: tadbit: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git. [version]: Use "2.0.0" instead of "2.0".
2018-11-07gnu: filevercmp: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git. [arguments]: Add #T to the end of the install phase.
2018-11-07gnu: ritornello: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1. [arguments]: Adjust file patching.
2018-11-07gnu: ritornello: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07gnu: snap-aligner: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git. [arguments]: Use INVOKE.
2018-11-07gnu: sortmerna: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07gnu: vsearch: Fetch source from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07gnu: preseq: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
2018-11-07gnu: preseq: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07gnu: seqtk: Update to 1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3. [source]: Remove outdated snippet. [arguments]: Use INVOKE and return #T unconditionally.
2018-11-07gnu: seqtk: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07gnu: raxml: Update to 8.2.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
2018-11-07gnu: python2-biom-format: Fix build.Ricardo Wurmus
This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa. * gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify phases of base package.
generated by cgit