Quest and Kellogg Linux Cluster Downtime, December 14 - 18.
Quest, including the Quest Analytics Nodes, the Genomics Compute Cluster (GCC), the Kellogg Linux Cluster (KLC), and Quest OnDemand, will be unavailable for scheduled maintenance starting at 8 A.M. on Saturday, December 14, and ending approximately at 5 P.M. on Wednesday, December 18. During the maintenance window, you will not be able to login to Quest, Quest Analytics Nodes, the GCC, KLC, or Quest OnDemand submit new jobs, run jobs, or access files stored on Quest in any way including Globus. For details on this maintenance, please see the Status of University IT Services page.
Quest RHEL8 Pilot Environment - November 18.
Starting November 18, all Quest users are invited to test and run their workflows in a RHEL8 pilot environment to prepare for Quest moving completely to RHEL8 in March 2025. We invite researchers to provide us with feedback during the pilot by contacting the Research Computing and Data Services team at quest-help@northwestern.edu. The pilot environment will consist of 24 H100 GPU nodes and seventy-two CPU nodes, and it will expand with additional nodes through March 2025. Details on how to access this pilot environment will be published in a KB article on November 18.
Downloading data from the Genomic Data Commons onto Quest via gdc-client
Genomic Data Commons
The National Cancer Institute's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine.
To download genomics data from the Genomic Data Commons onto Quest, PIs must have an electronic Research Administration (eRA) commons account from the National Institutes of Health that has been given DBGap access for the Genomic Data Commons. Once this access has been granted by the NIH, PIs can then disseminate Genomic Data Commons access to other individuals in their lab. De-identified data can then be downloaded from the Genomics Data Portal onto Quest into the PI's allocation for computational research purposes, using gdc-client.
Using gdc-client
At the command line on Quest in the directory that you'd like to transfer the Genomic Data Commons data into, type:
module load gdc-client
Help is available by typing:
gdc-client --help
Additional instructions for using gdc-client can be found on the National Cancer Institute's webinar on using the GDC Data Transfer Tool.