How to a Bioconductor repository
Bioconductor package repositories may be mirrored with rsync. This
is appropriate if you or your user community requires frequent local
access to many packages, where access to the main repository would be
expensive or impossible (e.g., because users can only access
repositories behind a firewall).
SSH key and IP address for rsync
Using rsync requires that you provide Bioconductor with minimal information
that includes (a) with an ssh public key and (b) the IP address(es) from which
you will perform rsync. If you would like to request rsync access please fill
out this google form: private mirror/rsync request form
Public mirrors
A mirror is considered “public” if it is an option in R’s
chooseBioCmirror() function and listed on our mirrors
page. Public mirrors must support https on their
site. If you are interested in hosting a publicly available mirror
site, please fill out this google form: public Bioc mirror request form
Structure of the rsync command
The overall structure of the rsync command is
rsync SSH_OPTION -e "ssh -i /path/to/ssh" [OPTIONS] SRC DEST
SSH_OPTION is required, and tells rsync to use SSH during the
transfer. An appropriate command might be
-e "ssh -i ~/.ssh/"
This can often be abbreviated to -e "ssh", and customized through an
SSH config file.
[OPTIONS] determine how files are synchronized with the server. For
a mirror, appropriate values are -zrtlv --delete.
SRC consists of the account and host for the connection, and the
path on the host to the hierarchy to be synchronized. For instance, to
synchronize the software packages on the current release branch one would use
bioc-rsync@master.bioconductor.org:3.15/bioc
DEST is the location on the local file system of the synchronized
repository, e.g.,
~/bioconductor_repositories/3.15/bioc
Thus a complete command might be
rsync -e "ssh -i ~/.ssh" -zrtlv --delete \
bioc-rsync@master.bioconductor.org:3.15/bioc \
~/bioconductor_repositories/3.15/bioc
Example: rsync an entire Bioconductor release
This is appropriate if you are providing your user community with a version of the entire Bioconductor release, with software, data annotation, and data experiment packages. The following uses Bioconductor version 3.15, the current release.
Directory structure
Pick a destination directory where files will be mirrored. Let’s say
this will be in /dest. This directory should be served by your web
server. Under that you’ll need a directory called packages. This
directory must be present as it is part of the structure of a
Bioconductor repository. Underneath packages should be a directory
corresponding to the versions of Bioconductor that you will host. The
current release version is 3.15 and the
current devel version is 3.16. We recommend
you use symlinks called release and 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 exact dates).
The following commands will create the directory structure you’ll need
(remember that /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/3.15 # current release
mkdir /dest/packages/3.16 # current devel
ln -s /dest/packages/3.15 /dest/packages/release # change these links
ln -s /dest/packages/3.15 /dest/packages/devel # every 6 months (with Bioc release)
rsync the Bioconductor release repository
To synchronize an entire release, use the command
rsync -e "ssh" -zrtlv --delete bioc-rsync@master.bioconductor.org:release /dest/packages/release
It is also possible to separately synchronize just the software packages…
rsync -e "ssh" -zrtlv --delete bioc-rsync@master.bioconductor.org:release/bioc /dest/packages/release/bioc
…or the data annotation and data experiment packages
rsync -e "ssh" -zrtlv --delete bioc-rsync@master.bioconductor.org:release/data /dest/packages/release/data
rsync the Bioconductor devel repository
To mirror all Bioconductor ‘devel’ (version 3.16) repositories:
rsync -e "ssh" -zrtlv --delete bioc-rsync@master.bioconductor.org:devel /dest/packages/devel
Bioconductor devel software repository:
rsync -e "ssh" -zrtlv --delete bioc-rsync@master.bioconductor.org:devel/bioc /dest/packages/devel/bioc
Bioconductor devel annotation and experiment data repositories:
rsync -e "ssh" -zrtlv --delete bioc-rsync@master.bioconductor.org:devel/data /dest/packages/devel/data
Additional information
Make sure the directory above packages is served by a web server.
Bioconductor is big (> 188GB for BioC 3.16).
Please check the size of what will be transferred with e.g. rsync -e "ssh"
-avn bioc-rsync@master.bioconductor.org:release and make sure you have enough
room on your local disk before you start.
It is recommended that package repositories be synchronized 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.
The Bioconductor master package repositories reside at https://master.bioconductor.org in the Amazon cloud.
