| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2018-07-29 | gnu: python-dendropy: Update to 4.4.0....* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy):
Update to 4.4.0.
[source]: Use GitHub URI. Remove patch.
[properties]: Remove field.
(python2-dendropy)[arguments]: Run tests with setup.py.
[native-inputs]: Remove 'python2-nose.
* gnu/packages/patches/python-dendropy-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Delete it.
| Ben Woodcroft |
| 2018-07-29 | gnu: Add python-fastalite....* gnu/packages/bioinformatics.scm (python-fastalite, python2-fastalite):
New variables.
| Ben Woodcroft |
| 2018-07-27 | gnu: pigx-scrnaseq: Disable another expensive test....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc
test.
| Ricardo Wurmus |
| 2018-07-27 | gnu: Add snakemake-4....* gnu/packages/python.scm (snakemake-4): New variable.
* gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq,
pigx-chipseq)[inputs]: Use it.
| Ricardo Wurmus |
| 2018-07-26 | gnu: java-picard: Fix manifest....* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Adjust phase
'edit-classpath-in-manifest for the new manifest generation code.
| Gábor Boskovits |
| 2018-07-09 | gnu: macs: Update to 2.1.1.20160309....* gnu/packages/bioinformatics.scm (macs): Update to 2.1.1.20160309.
| Ricardo Wurmus |
| 2018-07-05 | gnu: pigx: Update to 0.0.3....* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.3.
| Ricardo Wurmus |
| 2018-07-05 | gnu: r-getopt: Move from bioinformatics to cran....* gnu/packages/bioinformatics.scm (r-getopt): Move from here...
* gnu/packages/cran.scm (r-getopt): ...to here.
| Ricardo Wurmus |
| 2018-07-05 | gnu: pigx-scrnaseq: Update to 0.0.6....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.6.
[arguments]: Remove "wrap-executable" phase.
| Ricardo Wurmus |
