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* 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.
* gnu: r-complexheatmap: Update to 1.18.1.Ricardo Wurmus2018-06-21
| | | | * gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.1.
* gnu: r-delayedarray: Update to 0.6.1.Ricardo Wurmus2018-06-21
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.1.
* gnu: r-optparse: Update to 1.6.0.Ricardo Wurmus2018-06-21
| | | | * gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.0.
* gnu: r-biocviews: Update to 1.48.2.Ricardo Wurmus2018-06-21
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.2.
* gnu: pigx-chipseq: Update to 0.0.16.Ricardo Wurmus2018-06-16
| | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16.
* gnu: Add minimap2.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/bioinformatics.scm (minimap2): New variable.
* gnu: pigx-bsseq: Update to 0.0.9.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
* gnu: pigx-scrnaseq: Update to 0.0.5.Ricardo Wurmus2018-06-13
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic.
* gnu: r-seurat: Update to 2.3.2.Ricardo Wurmus2018-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2. [propagated-inputs]: Add r-hdf5r.
* gnu: r-s4vectors: Update to 0.18.3.Ricardo Wurmus2018-06-13
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
* gnu: r-biocviews: Update to 1.48.1.Ricardo Wurmus2018-06-13
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
* gnu: rcas-web: Update to 0.0.5.Ricardo Wurmus2018-06-08
| | | | * gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.5.
* gnu: r-rcas: Update to 1.6.0.Ricardo Wurmus2018-06-07
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0. [source]: Fetch from bioconductor. [native-inputs]: Remove r-knitr. [propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi, r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.
* gnu: star: Update to 2.6.0c.Ricardo Wurmus2018-06-07
| | | | | * gnu/packages/bioinformatics.scm (star): Update to 2.6.0c. [source]: Fetch from git.
* Merge branch 'master' into core-updatesRicardo Wurmus2018-06-05
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| * gnu: Add sjcount.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/bioinformatics.scm (sjcount): New variable.
* | gnu: dropseq-tools: Remove failing phase.Ricardo Wurmus2018-06-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete "generate-jar-indices" phase.
* | gnu: pigx-scrnaseq: Use only one variant of Picard.Ricardo Wurmus2018-06-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace "java-picard" with "java-picard-2.10.3".
* | gnu: java-picard: Delete failing build phase.Ricardo Wurmus2018-06-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete "generate-jar-indices" phase.
* | gnu: java-picard-1.113: Delete failing build phase.Ricardo Wurmus2018-06-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete "generate-jar-indices" build phase.
* | gnu: java-picard-2.10.3: Delete failing build phase.Ricardo Wurmus2018-06-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete generate-jar-indices phase.
* | Merge branch 'master' into core-updatesRicardo Wurmus2018-06-05
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| * gnu: r-rtracklayer: Update to 1.40.3.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
| * gnu: r-methylkit: Update to 1.6.1.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
| * gnu: r-bamsignals: Update to 1.12.1.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
* | Merge branch 'master' into core-updatesRicardo Wurmus2018-06-02
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| * gnu: r-scater: Update to 1.8.0.Ricardo Wurmus2018-06-02
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0. [propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove r-matrixstats and r-biomart.
| * gnu: r-scran: Update to 1.8.2.Ricardo Wurmus2018-06-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2. [propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
| * gnu: r-delayedmatrixstats: Update to 1.2.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
| * gnu: r-singlecellexperiment: Update to 1.2.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
| * gnu: r-beachmat: Update to 1.2.1.Ricardo Wurmus2018-06-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1. [inputs]: Add zlib.
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