beagle_cli

Beagle API Command Line Utility

Setup

• Requirements

  • python 3

• Instructions

  • pip install -r requirements.txt

• Run

  • ./beaglecli

Optional

You can export BEAGLE_USER and BEAGLE_PW environment variables to override interactive login.

To access other endpoints, export the environment variable BEAGLE_ENDPOINT.

Usage

  beaglecli files create <file_path> <file_type> <file_group_id> [--metadata-path=<metadata_path>] [--size=<size>]
  beaglecli files update <file_id> [--file-path=<file_path>] [--file-type=<file_type>] [--file-group=<file_group_id>] [--metadata-path=<metadata_path>] [--size=<size>]
  beaglecli files patch <file_id> [--file-path=<file_path>] [--file-type=<file_type>] [--file-group=<file_group_id>] [--metadata=<metadata>]... [--size=<size>]
  beaglecli files list [--page-size=<page_size>] [--path=<path>]... [--metadata=<metadata>]... [--file-group=<file_group>]... [--file-name=<file_name>]... [--filename-regex=<filename_regex>]
  beaglecli files delete --file-id=<file_id>...
  beaglecli sample create <sample-id>
  beaglecli sample list [--sample-id=<sample-id>]
  beaglecli sample redact <sample-id> [--value=<redact>]
  beaglecli storage create <storage_name>
  beaglecli storage list
  beaglecli file-types create <file_type>
  beaglecli file-types list
  beaglecli file-group create <file_group_name> <storage>
  beaglecli file-group list [--page-size=<page_size>]
  beaglecli etl delete --job-id=<job_id>...
  beaglecli run list [--page-size=<page_size>] [--request-id=<request_id>]... [--tags=<tags>]... [--job-groups=<job_groups>]... [--jira-ids=<jira_ids>]...
  beaglecli run latest-info [--request-id=<request_id | request_ids.csv>] [--job-group=<job_group>] [--jira-id=<jira_id>] [--output-file=<output_file>] [--completed] [--page-size=<page_size>] [--metadata-only] [--max-pages]
  beaglecli run get <run_id>
  beaglecli run submit-request --pipeline=<pipeline> [--request-ids=<request_ids>] [--job-group-id=<job_group_id>] [--for-each=<True or False>]
  beaglecli run submit-runs --pipelines=<pipeline>... --versions=<versions>...[--run-file=<run_file>] [--run-ids=<run_ids>]... [--job-group-id=<job_group_id>] [--for-each=<True or False>]
  beaglecli import-requests --request-ids=<request_id>... [--redelivery=<redelivery>]
  beaglecli tempo-mpgen
  beaglecli tempo-mpgen override --normals=<normal_samples> --tumors=<tumor_samples>
  beaglecli lims metadata [--request-id=<request_id>]
  beaglecli access link [--single-dir] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<msi|cnv|sv|snv|bams|nucleo>]... [--delete]
  beaglecli access link-patient [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<msi|cnv|sv|snv|bams|nucleo>]... [--delete]
  beaglecli cmoch link [--single-dir] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<bams>]... [--delete]
  beaglecli cmoch link-patient [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<bams>]... [--delete]
  beaglecli --version

Examples:

• List files by the sampleId

  beaglecli files list --metadata=sampleId:07973_BO_6
  
  

• Create registration of file into Beagle database

  beaglecli files create /path/to/fastq/file fastq 12345 --metadata-path=metadata.json
  

• Submit a run request of two request Ids through a pipeline called "argos", using an existing job_group_id:

  beaglecli run submit-request --pipeline=argos --request-ids=ABCDE_1,ABCDE_2 --job-group-id=FGHIJK-LMNOP-QRSTUV-WXY --job-group-id=FGHIJK-LMNOP-QRSTUV-WXYZ
  

• Return only the output metadata info for a given request id from the run api

  run latest-info --request-id 10101_A --completed --output-metadata-only --max-pages
  

• Return only the output metadata info for multiple request ids

  beaglecli run latest-info --request-id requests.txt --completed --output-metadata-only --max-pages
  

• Return and clean output metadata for a given request id from files api

  beaglecli files list --metadata=igoRequestId:13167_C  --file-type fastq --all --packaged
  

Note: Use requests.txt as a template for providing a multiple request ids

Troubleshooting

If you're having issues, try deleting ~/.beagle.conf file and logging back in.

For any other issues, please contact CMO Informatics (bolipatc@mskcc.org).