ACCESS TCGA DATA ON CAVATICA
Note: documentation links for TCGA data on Cavatica will be fully live on Oct. 10th. Thank you for your patience
The Cancer Genome Atlas (TCGA) is now available on Cavatica through an integration with the Seven Bridges Cancer Genomics Cloud (CGC). As such, the CGC is the source for authenticating users with the Database of Genotypes and Phenotypes (dbGaP) and authorizing access to TCGA data on Cavatica. To access TCGA on Cavatica, you will first be directed to create an account on the CGC.
You can access TCGA Open Data on Cavatica after you are authenticated via the CGC and agree to data use policies. In addition, you can obtain access to Controlled Data through a dbGaP application. If you have an approved dbGaP application, be sure update your application to list Seven Bridges as the Platform as a Service (PaaS). Security is our priority at Seven Bridges, and we ask that you familiarize yourself with and comply by TCGA data access standards on Cavatica.
Once you have TCGA access, check out the Data Browser to start querying TCGA data right away.
JOB.TREE.LOG FOR JOB EXECUTIONS
After each job execution, Cavatica will generate a job.tree.log file. This file contains the structure of the working directory and can be useful in the debugging process. Learn more from our documentation on the Seven Bridges Knowledge Center.