From d0bd632f89e242a2a217d7e85194589f088f75ea Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 16 Dec 2015 14:45:28 +0100
Subject: 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.
---
 doc/guix.texi | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

(limited to 'doc/guix.texi')

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
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