gnu: diamond: Update to 0.9.12.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.12.

gnu: multiqc: Update to 1.3.

* gnu/packages/bioinformatics.scm (multiqc): Update to 1.3.
[propagated-inputs]: Add python-enum34.
[license]: The license was changed to "GPLv3 or later" with this release.

gnu: r-ape: Update to 5.0.

* gnu/packages/bioinformatics.scm (r-ape): Update to 5.0.
[propagated-inputs]: Add r-rcpp.

gnu: vsearch: Update to 2.5.2.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.2.

gnu: diamond: Update to 0.9.11.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.11.

gnu: Remove cufflinks.

Cufflinks includes essential non-free code.
Fixes <https://bugs.gnu.org/28946>.

* gnu/packages/bioinformatics.scm (cufflinks): Remove variable.

gnu: vsearch: Update to 2.5.1.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.1.

gnu: bwa: Update to 0.7.17.

* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.17.

gnu: bwa: Change source URL to GitHub.

* gnu/packages/bioinformatics.scm (bwa)[source]: Change source URL to
GitHub.

gnu: miso: Update to 0.5.4.

* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4.

Use HTTPS for bioconductor.org.

* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.

gnu: f-seq: Fix location of commons-cli.jar.

* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Fix location of
commons-cli.jar in the wrapper script.

gnu: python-biopython: Update to 1.70.

* gnu/packages/python.scm (python-biopython, python2-biopython): Update to 1.70.

gnu: Add plink-ng.

* gnu/packages/bioinformatics.scm (plink-ng): New variable.

gnu: Add paml.

* gnu/packages/bioinformatics.scm (paml): New variable.

gnu: clustal-omega: Update to 1.2.4.

* gnu/packages/bioinformatics.scm (clustal-omega): Update to 1.2.4.

gnu: f-seq: Truncate version string.

* gnu/packages/bioinformatics.scm (f-seq)[version]: Truncate commit part of
the version string.

gnu: rcas-web: Update to 0.0.4.

* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.4.

Merge branch 'staging'

Merge branch 'master' into staging