| Age | Commit message (Expand) | Author |
|---|
| 2018-11-08 | gnu: tadbit: Fetch sources from git....* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
| Ricardo Wurmus |
| 2018-11-07 | gnu: filevercmp: Fetch sources from git....* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ritornello: Update to 2.0.1....* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ritornello: Fetch sources from git....* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: snap-aligner: Fetch sources from git....* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
| Ricardo Wurmus |
| 2018-11-07 | gnu: sortmerna: Fetch sources from git....* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: vsearch: Fetch source from git....* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: preseq: Update to 2.0.3....* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
| Ricardo Wurmus |
| 2018-11-07 | gnu: preseq: Fetch sources from git....* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: seqtk: Update to 1.3....* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
| Ricardo Wurmus |
| 2018-11-07 | gnu: seqtk: Fetch sources from git....* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: raxml: Update to 8.2.12....* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python2-biom-format: Fix build....This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa.
* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
| Ricardo Wurmus |
| 2018-11-07 | gnu: raxml: Fetch sources from git....* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: pyicoteo: Fetch sources from git....* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: sra-tools: Fetch sources from git....* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: libgff: Fetch sources from git....* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: kentutils: Fetch sources from git....* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-seqgl: Fetch sources from git....* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: pplacer: Fetch sources from git....* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
| Ricardo Wurmus |
| 2018-11-07 | gnu: minced: Update to 0.3.2....* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
| Ricardo Wurmus |
| 2018-11-07 | gnu: minced: Fetch sources from git....* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: metabat: Fetch sources from git....* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: mash: Update to 2.1....* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
| Ricardo Wurmus |
| 2018-11-07 | gnu: mash: Fetch sources from git....* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: kaiju: Update to 1.6.3....* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
| Ricardo Wurmus |
| 2018-11-07 | gnu: kaiju: Fetch sources from git....* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
| Ricardo Wurmus |
| 2018-11-07 | gnu: idr: Fetch sources from git....* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: java-htsjdk: Fetch sources from git....* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: hisat2: Use versioned source URL....* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
| Ricardo Wurmus |
| 2018-11-07 | gnu: grit: Update to 2.0.5....* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
| Ricardo Wurmus |
| 2018-11-07 | gnu: grit: Fetch sources from git....* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: gemma: Update to 0.98....* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
| Ricardo Wurmus |
| 2018-11-07 | gnu: gemma: Fetch sources from git....* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: fxtract: Fetch sources from git....* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ribodiff: Fetch sources from git....* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python-biom-format: Update to 2.1.7....* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python-biom-format: Fetch source from git....* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bioawk: Fetch sources from git....* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bedtools-2.18: Fetch sources from stable URL....* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bamtools: Fetch sources from git....* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ngless: Install links to required tools....* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
| Ricardo Wurmus |
| 2018-11-07 | gnu: prodigal: Fetch sources from git....* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-mzr: Update to 2.16.0....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-rhdf5lib: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-hdf5array: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-rhdf5: Update to 2.26.0....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-rcas: Update to 1.8.0....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-delayedmatrixstats: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-scran: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
| Ricardo Wurmus |
