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1356 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice eeb8b0e631
gnu: Use more HTTPS. 
* 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.
 2018-06-22 22:00:24 +02:00
Ricardo Wurmus c57e50b2b9
gnu: pigx-chipseq: Update to 0.0.17. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.17.
[arguments]: Remove "wrap-executable" phase.
 2018-06-22 11:40:27 +02:00
Ludovic Courtès 6fe419743d
Do not record store file name in bioinformatics.scm. 
* gnu/packages/bioinformatics.scm (dropseq-tools): Replace full store
file name with ellipses.
 2018-06-22 10:23:31 +02:00
Ricardo Wurmus 1f73fd017c
gnu: r-complexheatmap: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.1.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus a1c7016498
gnu: r-delayedarray: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.1.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus eafd35bad5
gnu: r-optparse: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.0.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus 1e2b2f41d7
gnu: r-biocviews: Update to 1.48.2. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.2.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus 901bcb7815
gnu: pigx-chipseq: Update to 0.0.16. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16.
 2018-06-16 12:11:09 +02:00
Ricardo Wurmus 53131eab2d
gnu: Add minimap2. 
* gnu/packages/bioinformatics.scm (minimap2): New variable.
 2018-06-14 13:51:15 +02:00
Ricardo Wurmus ce573b1128
gnu: pigx-bsseq: Update to 0.0.9. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
 2018-06-14 12:56:49 +02:00
Ricardo Wurmus 844cc1c8f3
gnu: pigx-scrnaseq: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5.
[inputs]: Add python-magic.
 2018-06-13 22:30:55 +02:00
Ricardo Wurmus 13b8dcf589
gnu: r-seurat: Update to 2.3.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2.
[propagated-inputs]: Add r-hdf5r.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 5b2a339e19
gnu: r-s4vectors: Update to 0.18.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 5b730eba3e
gnu: r-biocviews: Update to 1.48.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus cbc1c27b67
gnu: rcas-web: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.5.
 2018-06-08 17:39:24 +02:00
Ricardo Wurmus bcc2e0ed2e
gnu: r-rcas: Update to 1.6.0. 
* 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.
 2018-06-07 22:51:00 +02:00
Ricardo Wurmus 6d095c4cab
gnu: star: Update to 2.6.0c. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus ca8de35e90
Merge branch 'master' into core-updates 2018-06-05 23:44:11 +02:00
Ricardo Wurmus 909301591d
gnu: Add sjcount. 
* gnu/packages/bioinformatics.scm (sjcount): New variable.
 2018-06-05 15:42:44 +02:00
Ricardo Wurmus e53152c72d
gnu: dropseq-tools: Remove failing phase. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 13:12:13 +02:00
Ricardo Wurmus 9cc66d75a2
gnu: pigx-scrnaseq: Use only one variant of Picard. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"java-picard" with "java-picard-2.10.3".
 2018-06-05 11:26:34 +02:00
Ricardo Wurmus 1f94ba9408
gnu: java-picard: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 11:26:08 +02:00
Ricardo Wurmus a993ad833e
gnu: java-picard-1.113: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete
"generate-jar-indices" build phase.
 2018-06-05 11:15:21 +02:00
Ricardo Wurmus e847f402c1
gnu: java-picard-2.10.3: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete
generate-jar-indices phase.
 2018-06-05 11:14:38 +02:00
Ricardo Wurmus d7e6fb6d7e
Merge branch 'master' into core-updates 2018-06-05 11:09:39 +02:00
Ricardo Wurmus 71c495c941
gnu: r-rtracklayer: Update to 1.40.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus d19e0690b9
gnu: r-methylkit: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 0da6afa286
gnu: r-bamsignals: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus e0f8970357
Merge branch 'master' into core-updates 2018-06-02 13:44:43 +02:00
Ricardo Wurmus 92963798a6
gnu: r-scater: Update to 1.8.0. 
* 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.
 2018-06-02 13:42:05 +02:00
Ricardo Wurmus d7e3299987
gnu: r-scran: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2.
[propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus 8ec56b2956
gnu: r-delayedmatrixstats: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d99e0938fa
gnu: r-singlecellexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fd613234b7
gnu: r-beachmat: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e9c417361e
gnu: r-rhdf5lib: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1.
[arguments]: Adjust substitutions.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 0840352835
gnu: r-hdf5array: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 5cd725d002
gnu: r-qvalue: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus c6c619c179
gnu: r-hitc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 4dedecbe70
gnu: r-fithic: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 8db6256f4b
gnu: r-sushi: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 2d3c172b72
gnu: r-gwascat: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fecbbac286
gnu: r-gviz: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 6929b97583
gnu: r-gqtlstats: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0.
[propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 45c29a6e5c
gnu: r-ldblock: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 9b0b108ed9
gnu: r-erma: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0.
[propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and
r-iranges.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d26f95d079
gnu: r-snpstats: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus dcd1f0236c
gnu: r-gqtlbase: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e214a6e6ff
gnu: r-ggbio: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 34cc18d4de
gnu: r-biovizbase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 94ae875c0a
gnu: r-organismdbi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00