How to Create a Bioconductor Mirror Site

The Bioconductor package repositories may be mirrored with rsync. If you would like to become a mirror for package and data package repositories, please use the commands below.

BioC 2.14 repos

If you want to mirror the Bioconductor 2.14 repos (the current release version), please use the following commands:

All Bioconductor 2.14 repos

rsync -zrtlv --delete master.bioconductor.org::2.14 /dest/bioc_2.14

Bioconductor 2.14 Software repo

rsync -zrtlv --delete master.bioconductor.org::2.14/bioc /dest/bioc_2.14/bioc

Bioconductor 2.14 Data repos

rsync -zrtlv --delete master.bioconductor.org::2.14/data /dest/bioc_2.14/data

Bioconductor 2.14 Extra repo

rsync -zrtlv --delete master.bioconductor.org::2.14/extra /dest/bioc_2.14/extra

BioC 3.0 repos

If you want to mirror the Bioconductor 3.0 repos (the current devel version), please use the following commands:

All Bioconductor 3.0 repos

rsync -zrtlv --delete master.bioconductor.org::3.0 /dest/bioc_3.0

Bioconductor 3.0 Software repo

rsync -zrtlv --delete master.bioconductor.org::3.0/bioc /dest/bioc_3.0/bioc

Bioconductor 3.0 Data repos

rsync -zrtlv --delete master.bioconductor.org::3.0/data /dest/bioc_3.0/data

Bioconductor 3.0 Extra repo

rsync -zrtlv --delete master.bioconductor.org::3.0/extra /dest/bioc_3.0/extra

Additional information

Sync the above directories to a directory called packages on your system, and make sure the directory above packages is served by a web server.

Bioconductor is big (> 64G for BioC 2.14). Please check the size of what will be transferred with e.g. rsync -avn master.bioconductor.org::2.14 and make sure you have enough room on your local disk before you start.

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.

Finally, contact us if you would like to have your mirror listed on our mirror page and in R's chooseBioCmirror() function.

The Bioconductor master package repositories reside at Fred Hutchinson Cancer Research Center in Seattle, WA, USA.

Fred Hutchinson Cancer Research Center