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 the required configuration file(s). These include the irods_environment.json file pre-configured for your user account and an optional client-side server certificate file, if applicable.

To set up the environment, open your terminal, enter the directory where you saved the downloaded configuration file and ensure the iRODS configuration directory has been created:

$ mkdir -p ~/.irods

Next, either copy the returned irods_environment.json file to the directory:

$ cp irods_environment.json ~/.irods/

Alternatively, if you received an irods_config.zip archive from SODAR, unzip it into the configuration directory:

$ unzip irods_config.zip -d ~/.irods

Now you can initialize your connection to iRODS:

$ iinit

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

Note

If you log into SODAR using a single sign-on provider, you will have to generate a SODAR API token and use the token as your password when accessing iRODS and iRODS file links. You can create your API token in the API Tokens view.

Note

SODAR v1.0+ uses iRODS v4.3, which requires an updated client software and environment. If you experience connection issues, ensure you are running on the latest version iCommands or any other iRODS client(s) you use. You also need to download a new irods_environment.json file in the iRODS Info application. Alternatively, edit your existing JSON file and change the value of irods_authentication_scheme from PAM to pam_password.

See iRODS documentation for iCommands reference.

WebDAV

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.