Quest and Kellogg Linux Cluster Downtime, June 8th-14th, 2024.
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 7 A.M. on Saturday, June 8, and ending approximately at 5 P.M. on Friday, June 14. 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.
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.