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2017-05-13gnu: guile-json: Rename "guile2.2-json" to "guile-json".Ludovic Courtès
* gnu/packages/guile.scm (guile-json)[native-inputs]: Change GUILE-2.0 to GUILE-2.2. (guile2.2-json): Define using 'deprecated-package'. (guile2.0-json): New variable. * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Update accordingly. * gnu/packages/ci.scm (cuirass)[inputs]: Likewise. * gnu/packages/package-management.scm (guix)[inputs]: Likewise.
2017-05-10gnu: Add pplacer.Ben Woodcroft
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
2017-05-10gnu: Add taxtastic.Ben Woodcroft
* gnu/packages/bioinformatics.scm (taxtastic): New variable.
2017-05-02gnu: Avoid circular dependencies by Perl license.Petter
* guix/licenses.scm (perl-license): New variable. * gnu/packages/bioinformatics.scm: Change (package-license perl) to perl-license. * gnu/packages/compression.scm: Same. * gnu/packages/databases.scm: Same. * gnu/packages/gd.scm: Same. * gnu/packages/language.scm: Same. * gnu/packages/libevent.scm: Same. * gnu/packages/mail.scm: Same. * gnu/packages/messaging.scm: Same. * gnu/packages/ncurses.scm: Same. * gnu/packages/networking.scm: Same. * gnu/packages/photo.scm: Same. * gnu/packages/tcl.scm: Same. * gnu/packages/tex.scm: Same. * gnu/packages/tls.scm: Same. * gnu/packages/web.scm: Same. * gnu/packages/wm.scm: Same. * gnu/packages/xml.scm: Same. * gnu/packages/xorg.scm: Same. * gnu/packages/zip.scm: Same. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-05-01gnu: vcftools: Update to 0.1.15.Roel Janssen
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
2017-04-29gnu: r-genomeinfodbdata: Fix source url.Efraim Flashner
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use source uri and not bioconductor-uri shortener.
2017-04-28gnu: r-msnid: Update to 1.10.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
2017-04-28gnu: r-msnbase: Update to 2.2.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
2017-04-28gnu: r-pcamethods: Update to 1.68.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
2017-04-28gnu: r-mzid: Update to 1.14.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.14.0.
2017-04-28gnu: r-vsn: Update to 3.44.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-vsn): [source]: Update to 3.44.0, [propagated-inputs]: Add r-hexbin.
2017-04-28gnu: r-affy: Update to 1.54.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.54.0.
2017-04-28gnu: r-affyio: Update to 1.46.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.46.0.
2017-04-28gnu: r-mzr: Update to 2.10.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.10.0.
2017-04-28gnu: r-protgenerics: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.8.0.
2017-04-28gnu: r-sva: Update to 3.24.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.0.
2017-04-28gnu: r-copywriter: Update to 2.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.0.
2017-04-28gnu: r-chipseq: Update to 1.26.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.26.0.
2017-04-28gnu: r-rhdf5: Update to 2.20.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.20.0.
2017-04-28gnu: r-tximport: Update to 1.4.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.4.0.
2017-04-28gnu: r-mutationalpatterns: Update to 1.2.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): [source]: Update to 1.2.0, [propagated-inputs]: Add r-bsgenome-hsapiens-1000genomes-hs37d5, r-bsgenome-hsapiens-ucsc-hg19.
2017-04-28gnu: r-bamsignals: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.8.0.
2017-04-28gnu: r-rhtslib: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.8.0.
2017-04-28gnu: r-zlibbioc: Update to 1.22.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.22.0.
2017-04-28gnu: r-motifrg: Update to 1.20.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.20.0.
2017-04-28gnu: r-seqlogo: Update to 1.42.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.42.0.
2017-04-28gnu: r-genomation: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.8.0.
2017-04-28gnu: r-seqpattern: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.8.0.
2017-04-28gnu: r-impute: Update to 1.50.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.50.0.
2017-04-28gnu: r-bsgenome: Update to 1.44.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.44.0.
2017-04-28gnu: r-topgo: Update to 2.28.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.28.0.
2017-04-28gnu: r-graph: Update to 1.54.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.54.0.
2017-04-28gnu: r-genomicfeatures: Update to 1.28.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.0.
2017-04-28gnu: r-rtracklayer: Update to 1.36.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.0.
2017-04-28gnu: r-genomicalignments: Update to 1.12.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.0.
2017-04-28gnu: r-summarizedexperiment: Update to 1.6.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): [source]: Update to 1.6.0, [propagated-inputs]: Add r-delayedarray.
2017-04-28gnu: r-rsamtools: Update to 1.28.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.28.0.
2017-04-28gnu: r-biostrings: Update to 2.44.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.0.
2017-04-28gnu: r-biocparallel: Update to 1.10.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.0.
2017-04-28gnu: r-biomart: Update to 2.32.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.0.
2017-04-28gnu: r-annotationdbi: Update to 1.38.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.0.
2017-04-28gnu: r-biobase: Update to 2.36.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.0.
2017-04-28gnu: r-genomicranges: Update to 1.28.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.0.
2017-04-28gnu: r-xvector: Update to 0.16.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.16.0.
2017-04-28gnu: r-limma: Update to 3.32.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.0.
2017-04-28gnu: r-variantannotation: Update to 1.22.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.0.
2017-04-28gnu: r-edger: Update to 3.18.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.18.0.
2017-04-28gnu: r-genomeinfodb: Update to 1.12.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): [source] Update to 1.12.0, [propagated-inputs]: Add r-genomeinfodbdata.
2017-04-28gnu: r-iranges: Update to 2.10.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.0.
2017-04-28gnu: r-s4vectors: Update to 0.14.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.0.
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