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https://github.com/mskcc/beagle_cli
Beagle API Command Line Utility
https://github.com/mskcc/beagle_cli
Last synced: about 1 month ago
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Beagle API Command Line Utility
- Host: GitHub
- URL: https://github.com/mskcc/beagle_cli
- Owner: mskcc
- Created: 2020-01-14T22:20:21.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-09-10T19:34:01.000Z (3 months ago)
- Last Synced: 2024-09-10T22:22:33.666Z (3 months ago)
- Language: Python
- Size: 178 KB
- Stars: 0
- Watchers: 12
- Forks: 1
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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 [--metadata-path=] [--size=]
beaglecli files update [--file-path=] [--file-type=] [--file-group=] [--metadata-path=] [--size=]
beaglecli files patch [--file-path=] [--file-type=] [--file-group=] [--metadata=]... [--size=]
beaglecli files list [--page-size=] [--path=]... [--metadata=]... [--file-group=]... [--file-name=]... [--filename-regex=]
beaglecli files delete --file-id=...
beaglecli sample create
beaglecli sample list [--sample-id=]
beaglecli sample redact [--value=]
beaglecli storage create
beaglecli storage list
beaglecli file-types create
beaglecli file-types list
beaglecli file-group create
beaglecli file-group list [--page-size=]
beaglecli etl delete --job-id=...
beaglecli run list [--page-size=] [--request-id=]... [--tags=]... [--job-groups=]... [--jira-ids=]...
beaglecli run latest-info [--request-id=] [--job-group=] [--jira-id=] [--output-file=] [--completed] [--page-size=] [--metadata-only] [--max-pages]
beaglecli run get
beaglecli run submit-request --pipeline= [--request-ids=] [--job-group-id=] [--for-each=]
beaglecli run submit-runs --pipelines=... --versions=...[--run-file=] [--run-ids=]... [--job-group-id=] [--for-each=]
beaglecli import-requests --request-ids=... [--redelivery=]
beaglecli tempo-mpgen
beaglecli tempo-mpgen override --normals= --tumors=
beaglecli lims metadata [--request-id=]
beaglecli access link [--single-dir] [--request-id=] [--sample-id=] [--dir-version=] [--apps=]... [--delete]
beaglecli access link-patient [--request-id=] [--sample-id=] [--dir-version=] [--apps=]... [--delete]
beaglecli cmoch link [--single-dir] [--request-id=] [--sample-id=] [--dir-version=] [--apps=]... [--delete]
beaglecli cmoch link-patient [--request-id=] [--sample-id=] [--dir-version=] [--apps=]... [--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 ([email protected]).