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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-16 14:45:28 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-20 12:41:28 +0100
commitd0bd632f89e242a2a217d7e85194589f088f75ea (patch)
tree10ad2a7ba31c1a0a18f8c48c2d915e0fcc33bdb0 /doc
parent4c3d2b2a8f6f6249b497776e5513bbadf5c6aa4c (diff)
downloadguix-d0bd632f89e242a2a217d7e85194589f088f75ea.tar
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')
-rw-r--r--doc/guix.texi20
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