| Age | Commit message (Expand) | Author |
|---|
| 2018-09-14 | gnu: Add python-hic2cool.•••* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
| Ricardo Wurmus |
| 2018-09-10 | Adjust all users of (gnu packages ldc) to use (gnu packages dlang).•••This is a followup to commit 98d6543f86d01486c2f6e808eedd97c601ba3e7a.
* gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust
accordingly.
| Leo Famulari |
| 2018-09-10 | gnu: Add python-pygenometracks.•••* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-hicexplorer.•••* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-cooler.•••* gnu/packages/bioinformatics.scm (python-cooler): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-pyfaidx.•••* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-pypairix.•••* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
| Ricardo Wurmus |
| 2018-09-10 | gnu: Add python-intervaltree.•••* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
| Ricardo Wurmus |
| 2018-09-09 | gnu: r-annotationhub: Update to 2.12.1.•••* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
| Ricardo Wurmus |
| 2018-09-06 | Add missing use-modules clause.•••This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2.
Sorry!
* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-scrnaseq: Use latest version of Pandoc.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-bsseq: Use latest version of Pandoc.•••* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-chipseq: Use latest version of Pandoc.•••* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
| Ricardo Wurmus |
| 2018-09-05 | gnu: pigx-rnaseq: Use latest version of Pandoc.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.•••* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-graph: Move from bioinformatics to bioconductor.•••* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-scran: Update to 1.8.4.•••* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-scater: Update to 1.8.4.•••* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-hdf5array: Update to 1.8.1.•••* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-ggbio: Update to 1.28.5.•••* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-biovizbase: Update to 1.28.2.•••* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-keggrest: Update to 1.20.1.•••* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-edaseq: Update to 2.14.1.•••* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-seurat: Update to 2.3.4.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-msnbase: Update to 2.6.3.•••* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-maldiquant: Update to 1.18.•••* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-seqminer: Update to 6.1.•••* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-genomicfeatures: Update to 1.32.2.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-rtracklayer: Update to 1.40.6.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-delayedarray: Update to 0.6.5.•••* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-rsamtools: Update to 1.32.3.•••* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-biocparallel: Update to 1.14.2.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-genomicranges: Update to 1.32.6.•••* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-limma: Update to 3.36.3.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-variantannotation: Update to 1.26.1.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-edger: Update to 3.22.3.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-iranges: Update to 2.14.11.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-biocviews: Update to 1.48.3.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
| Ricardo Wurmus |
| 2018-09-05 | gnu: r-annotationforge: Update to 1.22.2.•••* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
| Ricardo Wurmus |
| 2018-09-05 | gnu: python-pybigwig: Update to 0.3.12.•••* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
| Ricardo Wurmus |
| 2018-09-05 | gnu: libbigwig: Update to 0.4.2.•••* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
| Ricardo Wurmus |
| 2018-09-03 | gnu: jellyfish: Update to 2.2.10.•••* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10.
[supported-systems]: Add aarch64-linux, mips64el-linux.
| Efraim Flashner |
| 2018-08-29 | gnu: Add gffcompare.•••gnu/packages/bioinformatics.scm (gffcompare): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
| pimi |
| 2018-08-29 | gnu: Add python-scanpy.•••* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
| Ricardo Wurmus |
| 2018-08-24 | gnu: Add find-circ.•••* gnu/packages/bioinformatics.scm (find-circ): New variable.
| Ricardo Wurmus |
| 2018-08-14 | gnu: Add gffread.•••* gnu/packages/bioinformatics.scm (gffread): New variable.
| Ricardo Wurmus |
| 2018-08-14 | gnu: Add r-circus.•••* gnu/packages/bioinformatics.scm (r-circus): New variable.
| Ricardo Wurmus |
| 2018-08-11 | Migrate search.cpan.org home pages to metacpan.org.•••The venerable search.cpan.org has retired[0].
[0]: https://log.perl.org/2018/05/goodbye-search-dot-cpan-dot-org.html
* guix/import/cpan.scm (cpan-home): Generate metacpan.org home page URIs.
Update all previously generated ones in (gnu packages) to their
canonical new homes.
| Tobias Geerinckx-Rice |
| 2018-08-03 | gnu: pigx-scrnaseq: Update to 0.0.7.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.7.
[inputs]: Add samtools.
| Ricardo Wurmus |
| 2018-07-29 | gnu: taxtastic: Add missing propagated-inputs.•••* gnu/packages/bioinformatics.scm (taxtastic)[propagated-inputs]: Add
python-psycopg2, python-fastalite, python-pyyaml, python-six, python-jinja2,
python-dendropy.
| Ben Woodcroft |
