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Galaxy Group

To begin using the Galaxy Group:

1.) Register for access to the SciCluster: https://hpc.umassmed.edu/wiki/index.php?title=Welcome_to_the_Scientific_Computing_for_Innovation_Cluster#OOD_Services

2.) Send an email to the Helpdesk and CC the HPCC-Admins requesting to join the Galaxy group.

3.) After you are added to the Galaxy group, you want to make sure you can access the services, run the programs and pipelines. Log in to our in-house galaxy mirror using your UMass Chan log in credentials.

4.) Galaxy Keys: To use the pipelines under UMass Tools in galaxy, you need to run a script in the cluster. This time you are going to use your HPCC user ID.

From your terminal, connect to the cluster:

  your_user@ghpcc06.umassrc.org

Run the script below;
/project/umw_biocore/bin/addKey.bash 

This is a one time script that will allow galaxy to submit future jobs to the cluster on your behalf. Send “the output” of this script to Biocore. We will make sure that you successfully added the keys to your cluster system.  

Next you will need to know, what you have in your directories in the cluster. There are three directories:

  • (~/galaxy directory) this will be your home directory for Rstudio
  • (~/galaxy/pub directory) this will be visible     from. http://galaxyweb.umassmed.edu/galaxy/your_cluster_user
  • (~/galaxy/pub/uploaddir directory) this can be used for larger files in galaxy

5.)    Project Space Requirements: Consult HPCC-Admins for your project space requirements. For example; typically 6 RNA-Seq libraries (5G to 10G each) require at least 500G of space to store the data and run the pipelines. Confirm you have the necessary space for your project.