The Bioconductor package repositories may be mirrored with
you would like to become a mirror for package and data package
repositories, please use the commands below.
Note that mirroring can also be accomplished with the
udr command. If you have installed
udr locally, you can just prepend
udr to the
rsync commands below.
This should result in a massive increase in file transfer speed.
The mirroring instructions at UCSC provide more details, including information
on firewall ports that may need to be opened at your instution in order
udr to work.
If you want to mirror the current Bioconductor release version (currently 3.0), please use the following commands:
Pick a destination directory where files will be mirrored. Let’s say this will be in
This directory should be served by your web server.
Under that you’ll need a directory called
This directory must be present as it is part of the structure
of a Bioconductor repository.
packages should be a directory corresponding to
the versions of Bioconductor that you will host. The current
release version is 3.0 and the current
devel version is 3.1. We recommend you
use symlinks called
devel that always point to
the current release and devel versions; this way you will never
have to change your rsync commands. But you should change the
symlink targets with every Bioconductor release (see
the release schedule for
commands will create the directory structure you’ll need (remember
/dest is just an example of the destination directory
you could use; you can put this directory anywhere on your system
where there is enough free space).
mkdir -p /dest/packages mkdir /dest/packages/3.0 # current release mkdir /dest/packages/3.1 # current devel ln -s /dest/packages/3.0 /dest/packages/release # change these links ln -s /dest/packages/3.0 /dest/packages/devel # every 6 months (with Bioc release)
rsync -zrtlv --delete master.bioconductor.org::release /dest/packages/release
rsync -zrtlv --delete master.bioconductor.org::release/bioc /dest/packages/release /bioc
rsync -zrtlv --delete master.bioconductor.org::release/data /dest/packages/release/data
rsync -zrtlv --delete master.bioconductor.org::release/extra /dest/packages/release/extra
If you want to mirror the Bioconductor devel repos (currently 3.1), please use the following commands:
rsync -zrtlv --delete master.bioconductor.org::devel /dest/packages/devel
rsync -zrtlv --delete master.bioconductor.org::devel/bioc /dest/packages/devel/bioc
rsync -zrtlv --delete master.bioconductor.org::devel/data /dest/packages/devel/data
rsync -zrtlv --delete master.bioconductor.org::devel/extra /dest/packages/devel/extra
Make sure the directory above
packages is served by
a web server.
Bioconductor is big (> 188GB for BioC 3.1). Please check the size of
what will be transferred with e.g.
rsync -avn master.bioconductor.org::release
and make sure you have enough room on your local disk before you
It is recommended that package repositories be synced once per day, scheduled with cron.
Begin using your new local repository, by making it accessible on your webserver. See the “contriburl” option to install.packages() (utils) for more information.