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* gnu: r-scran: Update to 1.8.4.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
* gnu: r-scater: Update to 1.8.4.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
* gnu: r-hdf5array: Update to 1.8.1.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
* gnu: r-ggbio: Update to 1.28.5.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5. [propagated-inputs]: Add r-rlang.
* gnu: r-biovizbase: Update to 1.28.2.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2. [propagated-inputs]: Add r-rlang.
* gnu: r-keggrest: Update to 1.20.1.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
* gnu: r-edaseq: Update to 2.14.1.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
* gnu: r-seurat: Update to 2.3.4.Ricardo Wurmus2018-09-05
| | | | | | | | | * 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.
* gnu: r-msnbase: Update to 2.6.3.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
* gnu: r-maldiquant: Update to 1.18.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
* gnu: r-seqminer: Update to 6.1.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
* gnu: r-genomicfeatures: Update to 1.32.2.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
* gnu: r-rtracklayer: Update to 1.40.6.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
* gnu: r-delayedarray: Update to 0.6.5.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
* gnu: r-rsamtools: Update to 1.32.3.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
* gnu: r-biocparallel: Update to 1.14.2.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
* gnu: r-genomicranges: Update to 1.32.6.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
* gnu: r-limma: Update to 3.36.3.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
* gnu: r-variantannotation: Update to 1.26.1.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
* gnu: r-edger: Update to 3.22.3.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
* gnu: r-iranges: Update to 2.14.11.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
* gnu: r-biocviews: Update to 1.48.3.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
* gnu: r-annotationforge: Update to 1.22.2.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
* gnu: python-pybigwig: Update to 0.3.12.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12. [propagated-inputs]: Add python-numpy.
* gnu: libbigwig: Update to 0.4.2.Ricardo Wurmus2018-09-05
| | | | | | | | * 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.
* gnu: jellyfish: Update to 2.2.10.Efraim Flashner2018-09-03
| | | | | * gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10. [supported-systems]: Add aarch64-linux, mips64el-linux.
* gnu: Add gffcompare.pimi2018-08-29
| | | | | | gnu/packages/bioinformatics.scm (gffcompare): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: Add python-scanpy.Ricardo Wurmus2018-08-29
| | | | * gnu/packages/bioinformatics.scm (python-scanpy): New variable.
* gnu: Add find-circ.Ricardo Wurmus2018-08-24
| | | | * gnu/packages/bioinformatics.scm (find-circ): New variable.
* gnu: Add gffread.Ricardo Wurmus2018-08-14
| | | | * gnu/packages/bioinformatics.scm (gffread): New variable.
* gnu: Add r-circus.Ricardo Wurmus2018-08-14
| | | | * gnu/packages/bioinformatics.scm (r-circus): New variable.
* Migrate search.cpan.org home pages to metacpan.org.Tobias Geerinckx-Rice2018-08-11
| | | | | | | | | | 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.
* gnu: pigx-scrnaseq: Update to 0.0.7.Ricardo Wurmus2018-08-03
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.7. [inputs]: Add samtools.
* gnu: taxtastic: Add missing propagated-inputs.Ben Woodcroft2018-07-29
| | | | | | * gnu/packages/bioinformatics.scm (taxtastic)[propagated-inputs]: Add python-psycopg2, python-fastalite, python-pyyaml, python-six, python-jinja2, python-dendropy.
* gnu: python-dendropy: Update to 4.4.0.Ben Woodcroft2018-07-29
| | | | | | | | | | | * 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.
* gnu: Add python-fastalite.Ben Woodcroft2018-07-29
| | | | | * gnu/packages/bioinformatics.scm (python-fastalite, python2-fastalite): New variables.
* gnu: pigx-scrnaseq: Disable another expensive test.Ricardo Wurmus2018-07-27
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc test.
* gnu: Add snakemake-4.Ricardo Wurmus2018-07-27
| | | | | | * gnu/packages/python.scm (snakemake-4): New variable. * gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq, pigx-chipseq)[inputs]: Use it.
* gnu: java-picard: Fix manifest.Gábor Boskovits2018-07-26
| | | | | * gnu/packages/bioinformatics.scm (java-picard)[arguments]: Adjust phase 'edit-classpath-in-manifest for the new manifest generation code.
* gnu: macs: Update to 2.1.1.20160309.Ricardo Wurmus2018-07-09
| | | | * gnu/packages/bioinformatics.scm (macs): Update to 2.1.1.20160309.
* gnu: pigx: Update to 0.0.3.Ricardo Wurmus2018-07-05
| | | | * gnu/packages/bioinformatics.scm (pigx): Update to 0.0.3.
* gnu: r-getopt: Move from bioinformatics to cran.Ricardo Wurmus2018-07-05
| | | | | * gnu/packages/bioinformatics.scm (r-getopt): Move from here... * gnu/packages/cran.scm (r-getopt): ...to here.
* gnu: pigx-scrnaseq: Update to 0.0.6.Ricardo Wurmus2018-07-05
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.6. [arguments]: Remove "wrap-executable" phase.
* gnu: Add r-loomr.Ricardo Wurmus2018-07-03
| | | | * gnu/packages/bioinformatics.scm (r-loomr): New variable.
* gnu: pigx-bsseq: Update to 0.0.10.Ricardo Wurmus2018-07-03
| | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.10. [arguments]: Remove "wrap-executable" phase.
* gnu: pigx-rnaseq: Update to 0.0.4.Ricardo Wurmus2018-07-03
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.4. [arguments]: Remove "wrap-executable" phase.
* gnu: pigx-chipseq: Update to 0.0.20.Ricardo Wurmus2018-07-03
| | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.20.
* gnu: Use more HTTPS.Tobias Geerinckx-Rice2018-06-22
| | | | | | | | | | | | * gnu/packages/admin.scm (net-base, wakelan, pam-krb5) [home-page]: Use HTTPS. (dfc, libpcap, tcpdump, wpa-supplicant-minimal, libcap-ng, audit) [source, home-page]: Likewise. * gnu/packages/algebra.scm (eigen)[home-page]: Likewise. (gp2c, pari-gp)[source, home-page]: Likewise. * gnu/packages/animation.scm (etl, synfig, synfigstudio, papagayo) [home-page]: Likewise. * gnu/packages/bioinformatics.scm (tadbit)[home-page]: Likewise.
* gnu: pigx-chipseq: Update to 0.0.17.Ricardo Wurmus2018-06-22
| | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.17. [arguments]: Remove "wrap-executable" phase.
* Do not record store file name in bioinformatics.scm.Ludovic Courtès2018-06-22
| | | | | * gnu/packages/bioinformatics.scm (dropseq-tools): Replace full store file name with ellipses.
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