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2018-09-10Adjust all users of (gnu packages ldc) to use (gnu packages dlang).Leo Famulari
This is a followup to commit 98d6543f86d01486c2f6e808eedd97c601ba3e7a. * gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust accordingly.
2018-09-10gnu: Add python-pygenometracks.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
2018-09-10gnu: Add python-hicexplorer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
2018-09-10gnu: Add python-cooler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
2018-09-10gnu: Add python-pyfaidx.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
2018-09-10gnu: Add python-pypairix.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
2018-09-10gnu: Add python-intervaltree.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
2018-09-09gnu: r-annotationhub: Update to 2.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
2018-09-06Add missing use-modules clause.Ricardo Wurmus
This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor).
2018-09-05gnu: pigx-scrnaseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-bsseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-chipseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-rnaseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
2018-09-05gnu: r-graph: Move from bioinformatics to bioconductor.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-graph): Move from here... * gnu/packages/bioconductor.scm (r-graph): ...to here.
2018-09-05gnu: r-scran: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
2018-09-05gnu: r-scater: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
2018-09-05gnu: r-hdf5array: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
2018-09-05gnu: r-ggbio: Update to 1.28.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5. [propagated-inputs]: Add r-rlang.
2018-09-05gnu: r-biovizbase: Update to 1.28.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2. [propagated-inputs]: Add r-rlang.
2018-09-05gnu: r-keggrest: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
2018-09-05gnu: r-edaseq: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
2018-09-05gnu: r-seurat: Update to 2.3.4.Ricardo Wurmus
* 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.
2018-09-05gnu: r-msnbase: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
2018-09-05gnu: r-maldiquant: Update to 1.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
2018-09-05gnu: r-seqminer: Update to 6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
2018-09-05gnu: r-genomicfeatures: Update to 1.32.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
2018-09-05gnu: r-rtracklayer: Update to 1.40.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
2018-09-05gnu: r-delayedarray: Update to 0.6.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
2018-09-05gnu: r-rsamtools: Update to 1.32.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
2018-09-05gnu: r-biocparallel: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
2018-09-05gnu: r-genomicranges: Update to 1.32.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
2018-09-05gnu: r-limma: Update to 3.36.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
2018-09-05gnu: r-variantannotation: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
2018-09-05gnu: r-edger: Update to 3.22.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
2018-09-05gnu: r-iranges: Update to 2.14.11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
2018-09-05gnu: r-biocviews: Update to 1.48.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
2018-09-05gnu: r-annotationforge: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
2018-09-05gnu: python-pybigwig: Update to 0.3.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12. [propagated-inputs]: Add python-numpy.
2018-09-05gnu: libbigwig: Update to 0.4.2.Ricardo Wurmus
* 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.
2018-09-03gnu: jellyfish: Update to 2.2.10.Efraim Flashner
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10. [supported-systems]: Add aarch64-linux, mips64el-linux.
2018-08-29gnu: Add gffcompare.pimi
gnu/packages/bioinformatics.scm (gffcompare): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2018-08-29gnu: Add python-scanpy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
2018-08-24gnu: Add find-circ.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (find-circ): New variable.
2018-08-14gnu: Add gffread.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gffread): New variable.
2018-08-14gnu: Add r-circus.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-circus): New variable.
2018-08-11Migrate search.cpan.org home pages to metacpan.org.Tobias Geerinckx-Rice
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.
2018-08-03gnu: pigx-scrnaseq: Update to 0.0.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.7. [inputs]: Add samtools.
2018-07-29gnu: taxtastic: Add missing propagated-inputs.Ben Woodcroft
* gnu/packages/bioinformatics.scm (taxtastic)[propagated-inputs]: Add python-psycopg2, python-fastalite, python-pyyaml, python-six, python-jinja2, python-dendropy.
2018-07-29gnu: python-dendropy: Update to 4.4.0.Ben Woodcroft
* 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.
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