| Age | Commit message (Expand) | Author |
|---|
| 2018-09-22 | gnu: hmmer: Update to 3.2.1....* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ben Woodcroft |
| 2018-09-21 | gnu: Add r-pore....* gnu/packages/bioinformatics.scm (r-pore): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| pimi |
| 2018-09-20 | gnu: rsem: Update to 1.3.1....* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 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 |
