Getting Data from iPlant/CyVerse

This is the quick tutorial to download data from CyVerse (previously known as iPlant) on HPC clusters using iRODS. iRODS may or may not be available as module on your cluster, and if available as a module load the module to use irods commands.

# search
module spider irods # or
module spider icommands
# load
module load <module name>

If the module is unavailable, you can either install it yourself following the guidelines here or skip installation by using the singularity container (and run these commands within the container)

#pull container
singularity pull --name irods.sif shub://mjstealey/singularity-irods-icommands
# use container
singularity shell --bind $PWD irods.sif
singularity> iinit

1. Login to your CyVerse account

Sometimes also referred as iRODS account, this is required to access private files from the CyVerse data store. This is done by logging in via iinit command. You only need this once per cluster. As it involves data transfer, the best practice recommends using the data transfer nodes on HPC.

$ iinit
One or more fields in your iRODS environment file (.irodsEnv) are
missing; please enter them.
Enter the host name (DNS) of the server to connect to: data.iplantcollaborative.org
Enter the port number: 1247
Enter your irods user name: <username>
Enter your irods zone: iplant
Those values will be added to your environment file (for use by
other i-commands) if the login succeeds.
Enter your current iRODS password:
#password won't be displayed

Now you are logged in. Although your working directory doesn’t change, all iCommands can now access the CyVerse datastore. You can logout anytime by typing iexit command.

Alternatively, you can save this information in ~/.irods/irodsEnv file as follows:

irodsHost data.iplantcollaborative.org
irodsPort 1247
irodsUserName <username>
irodsZone iplant
irodsPassword <your password>

This will let you connect automatically each time you want to login by just typing in iinit command. You can also exclude the last line (password), so that it will prompt only password for logging in.

2. Download files

Navigate to the desired location/directory and use iget command to download the desired file. You can also use any of the standard UNIX command by using i as prefix (eg., icp for copy, imv to move, ipwd to print working directory etc.,)

iget path/to/filename

If there are large number of files to be copied or you just want to sync 2 directories (local and iplant), you can also use rsync command. rsync synchronize the data between a local copy (local file system) and the copy stored in iRODS or between two iRODS copies. You can use rsync to either:

  • synchronization of data from the client’s local file system to iRODS
  • from iRODS to the local file system
  • from one iRODS path to another iRODS path

To synchronize (recursively) the data from the local directory foo1 to the iRODS collection foo2

irsync -r foo1 i:foo2

To synchronize (recursively) the data from the iRODS collection foo1 to the local directory foo2

irsync -r i:foo1 foo2

To synchronize (recursively) the data from the iRODS collection foo1 to another iRODS collection foo2

irsync -r i:foo1 i:foo2

Finally, if you want to transfer a single file from local host to remote (iplant), you can do it using iput command.

iput filename

A full list of irods commands can be found here

References

For more information, follow these links:


Further Reading


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