To begin using Dolphin services:
1.) Register for access to the HPCC (High Performance Computing Cluster). The registration form can be found at MGHPC. Once the HPCC Admins group receives your registration form, they will send an email to your PI requesting the PI’s permission to give you access. After it’s approved you will receive an email from the HPCC Admins group with your HPCC account user name.
2.) Send an email to the HPCC-Admins to set your accounts for dolphin.
3.) After your accounts set, you want to make sure you can access the services, run the programs and pipelines. Log in to dolphin.umassmed.edu using your UMMS log in credentials. (Your email username(lowercase) and password)
4.) Dolphin Keys: To use the pipelines in dolphin, you need to run a script in the cluster. To connect cluster use your HPCC user ID and password sent by HPCC Admins.
From your terminal, connect to the cluster:
Run the script below;
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.