CGC command line tool
The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is one of three pilot systems funded by the National Cancer Institute to explore the paradigm of colocalizing massive genomics datasets, like The Cancer Genomics Atlas (TCGA), alongside secure and scalable computational resources to analyze them.
CLI tool supports following operations
- List projects (https://docs.cancergenomicscloud.org/docs/list-all-your-projects)
- List files in project (https://docs.cancergenomicscloud.org/docs/list-files-in-a-project)
- Get file details (https://docs.cancergenomicscloud.org/docs/get-file-details)
- Update file details (https://docs.cancergenomicscloud.org/docs/update-file-details)
- Download file (https://docs.cancergenomicscloud.org/docs/get-download-url-for-a-file)
Sample usage
cgccli --token {token} projects list
cgccli --token {token} files list --project test/simons-genome-diversity-project-sgdp
cgccli --token {token} files stat --file {file_id}
cgccli --token {token} files update --file {file_id} name=bla
cgccli --token {token} files update --file {file_id} metadata.sample_id=asdasf
cgccli --token {token} files download --file {file_id} --dest /tmp/foo.bar