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Cloud Shell

1. Log into Discovery Environment

Log into CyVerse DE with your CyVerse credentials.

If you have not yet created an account, go to the User Portal and do so.

The Cloud Shell App is already pinned to the Discovery Environment Tool Bar (left side of screen):

Alternately, use the search to specify ‘Apps’ then type keyword Shell or Cloud Shell

You can see Cloud Shell listed when you expand the three bars Menu icon.

cloudshell-0

2. Launch analysis

cloudshell-1

Instant Launches start the App immediately without the opportunity to add any input data or increase the VM size.

Clicking on the Apps will show the Cloud Shell in “Featured Apps”.

By default the Analysis Name is the name of the App plus the date and time.

The output folder will use this same name and be written to the /iplant/home/username/analyses/ directory AFTER the interactive analysis is completed.

Note

Deleting a running Analysis will stop it from writing outputs to your data store analyses/ directory.

Note

The input files and/or folders can be selected under the ‘Parameters’ tab.

Tip

If you have an existing set of files or directories, you can import these into the app using input files and/or folder in the Parameters .

4. Activate a conda environment

The Cloud Shell comes with multiple languages and package managers pre-installed. These include go, python, and rust.

Package managers include conda and cargo in addition to linux apt and apt-get.

Your identity inside the container is user and you have limited sudo privileges to install new packages into the container.

These changes are not saved after the analyses ends, or when you start a new Cloud Shell Analyses later.

Tip

The cloud shell is running a terminal multiplexer called tmux which keeps your session active even after you’ve closed your browser tab.

tmux keyboard commands should function normally.

To activate conda:

` conda init `

and then

` conda activate base `

If you recieve a message about refreshing your screen, you can exit the cloud shell by typing “exit” and then hitting the refresh button on your browser tab.

5. Adding data to your analysis

To connect to the CyVerse DataStore, you can initiate an iRODS iCommands iinit

You should now be connected to your /iplant/home/username home directory.

ils

or

` ils /iplant/home/username/ `

To view the ‘shared’ directory try:

` ils /iplant/home/shared `

Download data into your Cloud Shell with iCommands by running iget

` iget -KPbvrf /iplant/home/shared/cyverse_training/ `

```

6. Complete and Save Outputs

After finishing your analyses, you can save the outputs back to Data Store.

You can either use iput to copy your new files back to your user space, or if you’ve left your new work in the /home/user/work folder, it will be copied back to your /iplant/home/username/Analyses/ directory.

You can find the outputs you generated (if any) using the same steps as before, but this time select the ‘Go To Output Folder’.

7. Terminate your app

The Discovery Environment is a shared system. In fairness to the community, we ask uses to “Terminate” any apps they have started when they are no longer running analyses.

In the Analyses window, select the app with the checkbox, then select “More Actions” and “Terminate” to shut the app down.

Any new data in the /home/user/work directory will begin copying back to your folder at this time.

Any input data which you added when the app started using the conventional launch feature will not be copied.

Warning

VICE apps only run for a pre-determined amount of time, typically between 4 and 48 hours. If you have opted for email notifications from DE, then you’ll get a notification 1 day before and 1 hour before the app gets terminated. If you want to extend the time, you need to login to https://de.cyverse.org, find your analysis and then click the hour glass which automatically extends the app run time.

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