{"id":19749473,"url":"https://github.com/mskcc/beagle_cli","last_synced_at":"2026-02-09T00:31:12.967Z","repository":{"id":39706948,"uuid":"233947299","full_name":"mskcc/beagle_cli","owner":"mskcc","description":"Beagle API Command Line Utility","archived":false,"fork":false,"pushed_at":"2026-02-04T01:14:11.000Z","size":222,"stargazers_count":1,"open_issues_count":11,"forks_count":1,"subscribers_count":9,"default_branch":"master","last_synced_at":"2026-02-04T09:27:16.884Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mskcc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-01-14T22:20:21.000Z","updated_at":"2025-11-25T15:39:10.000Z","dependencies_parsed_at":"2024-04-22T19:39:10.861Z","dependency_job_id":"6370347f-7991-4373-b1c1-a0688b6204d4","html_url":"https://github.com/mskcc/beagle_cli","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/beagle_cli","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fbeagle_cli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fbeagle_cli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fbeagle_cli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fbeagle_cli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/beagle_cli/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fbeagle_cli/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29251464,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-08T22:49:53.206Z","status":"ssl_error","status_checked_at":"2026-02-08T22:49:51.384Z","response_time":57,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-12T02:26:39.173Z","updated_at":"2026-02-09T00:31:12.950Z","avatar_url":"https://github.com/mskcc.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# beagle_cli\nBeagle API Command Line Utility\n\n#### Setup\n- Requirements\n  - `python 3`\n\n- Instructions\n  - `pip install -r requirements.txt`\n\n- Run\n  - `./beaglecli`\n\n\n##### Optional\n\nYou can export `BEAGLE_USER` and `BEAGLE_PW` environment variables to override interactive login.\n\nTo access other endpoints, export the environment variable `BEAGLE_ENDPOINT`.\n\n\n##### Usage\n```\n  beaglecli files create \u003cfile_path\u003e \u003cfile_type\u003e \u003cfile_group_id\u003e [--metadata-path=\u003cmetadata_path\u003e] [--size=\u003csize\u003e]\n  beaglecli files update \u003cfile_id\u003e [--file-path=\u003cfile_path\u003e] [--file-type=\u003cfile_type\u003e] [--file-group=\u003cfile_group_id\u003e] [--metadata-path=\u003cmetadata_path\u003e] [--size=\u003csize\u003e]\n  beaglecli files patch \u003cfile_id\u003e [--file-path=\u003cfile_path\u003e] [--file-type=\u003cfile_type\u003e] [--file-group=\u003cfile_group_id\u003e] [--metadata=\u003cmetadata\u003e]... [--size=\u003csize\u003e]\n  beaglecli files list [--page-size=\u003cpage_size\u003e] [--path=\u003cpath\u003e]... [--metadata=\u003cmetadata\u003e]... [--file-group=\u003cfile_group\u003e]... [--file-name=\u003cfile_name\u003e]... [--filename-regex=\u003cfilename_regex\u003e]\n  beaglecli files delete --file-id=\u003cfile_id\u003e...\n  beaglecli sample create \u003csample-id\u003e\n  beaglecli sample list [--sample-id=\u003csample-id\u003e]\n  beaglecli sample redact \u003csample-id\u003e [--value=\u003credact\u003e]\n  beaglecli storage create \u003cstorage_name\u003e\n  beaglecli storage list\n  beaglecli file-types create \u003cfile_type\u003e\n  beaglecli file-types list\n  beaglecli file-group create \u003cfile_group_name\u003e \u003cstorage\u003e\n  beaglecli file-group list [--page-size=\u003cpage_size\u003e]\n  beaglecli etl delete --job-id=\u003cjob_id\u003e...\n  beaglecli run list [--page-size=\u003cpage_size\u003e] [--request-id=\u003crequest_id\u003e]... [--tags=\u003ctags\u003e]... [--job-groups=\u003cjob_groups\u003e]... [--jira-ids=\u003cjira_ids\u003e]...\n  beaglecli run latest-info [--request-id=\u003crequest_id | request_ids.csv\u003e] [--job-group=\u003cjob_group\u003e] [--jira-id=\u003cjira_id\u003e] [--output-file=\u003coutput_file\u003e] [--completed] [--page-size=\u003cpage_size\u003e] [--metadata-only] [--max-pages]\n  beaglecli run get \u003crun_id\u003e\n  beaglecli run submit-request --pipeline=\u003cpipeline\u003e [--request-ids=\u003crequest_ids\u003e] [--job-group-id=\u003cjob_group_id\u003e] [--for-each=\u003cTrue or False\u003e]\n  beaglecli run submit-runs --pipelines=\u003cpipeline\u003e... --versions=\u003cversions\u003e...[--run-file=\u003crun_file\u003e] [--run-ids=\u003crun_ids\u003e]... [--job-group-id=\u003cjob_group_id\u003e] [--for-each=\u003cTrue or False\u003e]\n  beaglecli import-requests --request-ids=\u003crequest_id\u003e... [--redelivery=\u003credelivery\u003e]\n  beaglecli tempo-mpgen\n  beaglecli tempo-mpgen override --normals=\u003cnormal_samples\u003e --tumors=\u003ctumor_samples\u003e\n  beaglecli lims metadata [--request-id=\u003crequest_id\u003e]\n  beaglecli access link [--single-dir] [--request-id=\u003crequest_id\u003e] [--sample-id=\u003csample_id\u003e] [--dir-version=\u003cdir_version\u003e] [--apps=\u003cmsi|cnv|sv|snv|bams|nucleo\u003e]... [--delete]\n  beaglecli access link-patient [--request-id=\u003crequest_id\u003e] [--sample-id=\u003csample_id\u003e] [--dir-version=\u003cdir_version\u003e] [--apps=\u003cmsi|cnv|sv|snv|bams|nucleo\u003e]... [--delete]\n  beaglecli cmoch link [--single-dir] [--request-id=\u003crequest_id\u003e] [--sample-id=\u003csample_id\u003e] [--dir-version=\u003cdir_version\u003e] [--apps=\u003cbams\u003e]... [--delete]\n  beaglecli cmoch link-patient [--request-id=\u003crequest_id\u003e] [--sample-id=\u003csample_id\u003e] [--dir-version=\u003cdir_version\u003e] [--apps=\u003cbams\u003e]... [--delete]\n  beaglecli --version\n```\n Examples:\n- List files by the sampleId\n  ```\n  beaglecli files list --metadata=sampleId:07973_BO_6\n\n  ```\n- Create registration of file into Beagle database\n  ```\n  beaglecli files create /path/to/fastq/file fastq 12345 --metadata-path=metadata.json\n  ```\n- Submit a run request of two request Ids through a pipeline called \"argos\", using an existing job_group_id:\n  ```\n  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\n  ```\n- Return only the output metadata info for a given request id from the run api\n  ```\n  run latest-info --request-id 10101_A --completed --output-metadata-only --max-pages\n  ```\n- Return only the output metadata info for multiple request ids\n  ```\n  beaglecli run latest-info --request-id requests.txt --completed --output-metadata-only --max-pages\n  ```\n- Return and clean output metadata for a given request id from files api\n  ```\n  beaglecli files list --metadata=igoRequestId:13167_C  --file-type fastq --all --packaged\n  ```\nNote: Use `requests.txt` as a template for providing a multiple request ids\n\n#### Troubleshooting\n\nIf you're having issues, try deleting ~/.beagle.conf file and logging back in.\n\nFor any other issues, please contact CMO Informatics (bolipatc@mskcc.org).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fbeagle_cli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fbeagle_cli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fbeagle_cli/lists"}