Meant for:

  • iRODS admins
  • iRODS users

Requirements:

  • account on an iRODS instance
  • connected to iRODS, see How to connect to iRODS using iCommands
  • iCommands (iRODS CLI tool) installed (these tools are installed on all SURF HPC clusters: Lisa, Cartesius, Snellius, Spider)
  • all commands need to be run in a command line application


Note that in iRODS files are called data objects, and folders are called collections.

The iCommands have basic file handling functionality that have their (almost) equivalent in the Linux bash commands but with an 'i' prefix, *e.g.* 'ls' and 'ils', 'cp' and 'icp', 'mv' and 'imv', 'pwd' and 'ipwd', 'mkdir' and 'imkdir', 'cd' and 'icd'. 'rm' and 'irm'. Try out 'ihelp' if you want to know more about the available options.

However, please note that iRODS is not a filesystem like you have on your personal computer. Data handling is done differently.

Print current working directory and navigate to collections

Use 'ils' to see the collections (and data objects) available to you and navigate to a collection with 'icd':

ils

icd <collection name>


Note that you can't use bash tab completion with paths in iRODS. With either command you can use relative iRODS paths. The iCommands will use the current working iRODS collection to determine the absolute path. To see your current working directory:

ipwd

This information is also stored in a session file '.irods/irods_environment.$PID':

user@login:~$ cat .irods/irods_environment.json.14192 # the number is probably different in your case, try 'echo $$' to see what PID number your are using.
{
"irods_cwd": "/your/current/working/collection/in/iRODS"
}

By using 'icd', you are changing your current working directory and this file will be updated.

You can create collections with 'imkdir':

user@login:~$ imkdir new_collection_name

Again, this can be a relative path or an absolute path.

If you get an error that you are not allowed to create a collection, be sure to have navigated to a collection where you do have the permission to write.
To check the permissions of data objects and collections you can use:

ils -A

 ('-A' stands for Access Control Lists)

Learn more

More basic information concerning the use of iCommands (uploading/downloading files, sharing objects/collections, and querying metadata) can be found here under the heading 'Basic data/collection handling'.

  • No labels