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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-12-16 14:45:28 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-20 12:41:28 +0100 |
| commit | d0bd632f89e242a2a217d7e85194589f088f75ea (patch) | |
| tree | 10ad2a7ba31c1a0a18f8c48c2d915e0fcc33bdb0 /doc/guix.texi | |
| parent | 4c3d2b2a8f6f6249b497776e5513bbadf5c6aa4c (diff) | |
| download | guix-d0bd632f89e242a2a217d7e85194589f088f75ea.tar.gz | |
import: Add Bioconductor importer and updater.
* guix/import/cran.scm (%bioconductor-updater, latest-bioconductor-release, bioconductor-package?): New procedures. (cran->guix-package): Support repositories other than CRAN. (%bioconductor-url, %bioconductor-svn-url): New variables. (description->package): Update signature to distinguish between packages from different repositories. (latest-release): Rename procedure ... (latest-cran-release): ... to this. (cran-package?): Do not assume all R packages are available on CRAN. * tests/cran.scm: Update tests. * guix/scripts/import/cran.scm: Add "--archive" option and default to CRAN. * guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater". * doc/guix.texi: Document Bioconductor importer and updater.
Diffstat (limited to 'doc/guix.texi')
| -rw-r--r-- | doc/guix.texi | 20 |
1 files changed, 19 insertions, 1 deletions
diff --git a/doc/guix.texi b/doc/guix.texi index a3d751a296..2a97516084 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -4279,11 +4279,12 @@ guix import cpan Acme::Boolean @item cran @cindex CRAN +@cindex Bioconductor Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the central repository for the @uref{http://r-project.org, GNU@tie{}R statistical and graphical environment}. -Information is extracted from the package's DESCRIPTION file. +Information is extracted from the package's @code{DESCRIPTION} file. The command command below imports meta-data for the @code{Cairo} R package: @@ -4292,6 +4293,21 @@ R package: guix import cran Cairo @end example +When @code{--archive=bioconductor} is added, meta-data is imported from +@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R +packages for for the analysis and comprehension of high-throughput +genomic data in bioinformatics. + +Information is extracted from a package's @code{DESCRIPTION} file +published on the web interface of the Bioconductor SVN repository. + +The command command below imports meta-data for the @code{GenomicRanges} +R package: + +@example +guix import cran --archive=bioconductor GenomicRanges +@end example + @item nix Import meta-data from a local copy of the source of the @uref{http://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This @@ -4490,6 +4506,8 @@ the updater for GNOME packages; the updater for @uref{http://elpa.gnu.org/, ELPA} packages; @item cran the updater for @uref{http://cran.r-project.org/, CRAN} packages; +@item bioconductor +the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages; @item pypi the updater for @uref{https://pypi.python.org, PyPI} packages. @end table |