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* 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.
| * gnu: r-rhdf5lib: Update to 1.2.1.Ricardo Wurmus2018-06-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1. [arguments]: Adjust substitutions.
| * gnu: r-hdf5array: Update to 1.8.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
| * gnu: r-qvalue: Update to 2.12.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
| * gnu: r-hitc: Update to 1.24.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
| * gnu: r-fithic: Update to 1.6.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
| * gnu: r-sushi: Update to 1.18.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
| * gnu: r-gwascat: Update to 2.12.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
| * gnu: r-gviz: Update to 1.24.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
| * gnu: r-gqtlstats: Update to 1.12.0.Ricardo Wurmus2018-06-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0. [propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
| * gnu: r-ldblock: Update to 1.10.0.Ricardo Wurmus2018-06-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0. [propagated-inputs]: Add r-biocgenerics.
| * gnu: r-erma: Update to 0.12.0.Ricardo Wurmus2018-06-02
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0. [propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and r-iranges.
| * gnu: r-snpstats: Update to 1.30.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
| * gnu: r-gqtlbase: Update to 1.12.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
| * gnu: r-ggbio: Update to 1.28.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
| * gnu: r-biovizbase: Update to 1.28.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
| * gnu: r-organismdbi: Update to 1.22.0.Ricardo Wurmus2018-06-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
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