CyVerse

2 minute read

CyVersae is a NFS funded web platorm that has many pre defined apps. Mainly of the apps are for life sicence and can be very useful.

NOTE: Not suitable for jobs that require more than 12 CPU cores (ie. MPI).

Account

Go to CyVerse and click on Create Account.

There are a few steps, just fill in the fields accordingly and complete the forms.

After you have completed the form and submitted it, CyVerse will send you an email. Within the email will contain a link to set your password.

Data Management

There are a few ways to upload/download data, for example you can browse your files from the Discovery Environment. However here we will focus on the command line method, since that is directly supported on the HPC cluster. Please refer to here for additoinal methods.

First you will need to load the icommands tools:

module load icommands/4.1.10

Then you will need to initialize the connection to CyVerse:

iinit

When you run the above command it will ask a few questions about your connection:

Once the iinit command has completed you are now able to list, push, get files and folders on CyVerse directlry from the HPCC.

Upload

The basic format to push files to CyVerse is like so:

iput FileName CyVersePath

For example:

iput hg18.fasta .

Since you automatically start in your home directory from CyVerse, the . will just place the fasta file directly within your home.

Once that command completes, you can double check that the the does exist on CyVerse, by listing the files, like so:

ils

The ils and iput command will work with relative and absolute paths.

Download

The download method is identical to the upload method, just repalce iget instead of iput:

iget hg18.fasta .

The above command will download the hg18.fasta file to your current directory on the cluster.

Jobs

Jobs on CyVerse are deployed via apps that you launch through the GUI here. Here is s video explaining how to create a docker image on the CyVerse system as well as configure a custom app to use it.

Please contact support for help creating a custom app, or any other questions.