Before running an application, it is important to understand how data flows in and out of CyVerse with the Agave CLI. As a CyVerse user, you are able to store data in the central data store called data.iplantcollaborative.org. To see more information, use the following command:
systems-list -V data.iplantcollaborative.org
A “system” in Agave is a server or collection of servers associated with a single hostname. As you may see in the output from the above command, the CyVerse data store is a cloud-based repository from which data is accessed by all of its technologies. To make this your default data repository when using the Agave CLI, issue the command:
Now, when using the Agave CLI
files commands, you will automatically be configured to interact with this data storage system.
With the Agave CLI
files commands, you can list available files and directories, upload or download data, copy, move, or delete data, import data from another source, and change permissions on existing data.
To see a Linux-style long listing of what is currently available in your home directory, issue:
files-list -L username/
username is replaced with your CyVerse username.
If this is your first time interacting with the iPlant data store, then your home directory may still be empty.
Create a new folder in your home directory, then list the contents of that folder (empty for now) by typing:
files-mkdir -N new-folder username/ files-list -L username/ files-list -L username/new-folder/
Create an example file on your local machine, and upload it to the data store:
touch new-file.txt echo "some example text" >> new-file.txt files-upload -F new-file.txt username/ files-list -L username/
Many common Linux file manipulation commands, including
mv, have an analogous command in the Agave CLI:
files-copy -D username/new-file-copy.txt username/new-file.txt files-move -D username/new-folder/new-file-copy.txt username/new-file-copy.txt files-list -L username/ files-list -L username/new-folder/
Files and folders can be deleted, but be cautious because there is no way to recover:
files-delete username/new-folder/new-file-copy.txt files-delete username/new-folder/ files-list -L username/
Delete the local copy of
new-file.txt, then download the remote copy with the
rm new-file.txt files-get username/new-file.txt cat new-file.txt
This concludes the overview of how to manage data on the data storage system.
At any time, you can issue an Agave command with the
-h flag to find more information on the function and usage of the command.
Some advanced file operations will be demonstrated in the second part of this tutorial.
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