iRODS Access

Experiment data for omics project data is stored under a distributed iRODS server, which you can log on to with your Charité or MDC credentials. For accessing project data, membership in respective projects must be granted to you by a project owner or delegate.

For each project, sample data repository is located in the read-only sample_data collection. For uploading new files, you must create a landing zone as a temporary workspace. These are placed under the landing_zones collection. For more instructions, see the Landing Zones application under the project you are working on.

Command Line Access (Linux)

For command line access to iRODS, you should use iRODS iCommands in your Linux shell.

On the BIH Cluster, the required packages are already installed. If you need to access the data from elsewhere on the network, you need to install the irods-icommands package. See the official installation instructions for more information.

To configure your iCommands connection, open the iRODS Info application. In the app, click the Download Configuration button to download a configuration file archive. This archive contains the irods_environment.json file pre-configured for your user account. A server certificate file for secure connections is also included, if applicable.

Enter the directory where you saved the downloaded archive and enter the following commands:

mkdir -p ~/.irods
unzip -d ~/.irods

You will be prompted for your password, which is the same one you use to access this web site. After this, you should be successfully logged on to iRODS and can access data on the storage in your terminal.

See iRODS documentation for iCommands reference.


Project iRODS data can be accessed for through WebDAV by mounting it as a network drive or browsing it in read-only mode on a web browser. Links in SODAR UI provide shortcuts to specific collections and files on the WebDAV.