{"id":21287737,"url":"https://github.com/stjudecloud/msgenctl","last_synced_at":"2025-03-15T15:25:37.590Z","repository":{"id":65199175,"uuid":"398003665","full_name":"stjudecloud/msgenctl","owner":"stjudecloud","description":"CLI to manage Microsoft Genomics workflows","archived":false,"fork":false,"pushed_at":"2024-10-28T19:38:31.000Z","size":154,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-22T05:28:48.550Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Go","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/stjudecloud.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.txt","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}},"created_at":"2021-08-19T16:15:28.000Z","updated_at":"2024-10-28T19:38:35.000Z","dependencies_parsed_at":"2025-01-22T05:38:03.070Z","dependency_job_id":null,"html_url":"https://github.com/stjudecloud/msgenctl","commit_stats":{"total_commits":54,"total_committers":1,"mean_commits":54.0,"dds":0.0,"last_synced_commit":"6962bdd8c294bc91060c1d9577a937754e5bea1c"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmsgenctl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmsgenctl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmsgenctl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmsgenctl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stjudecloud","download_url":"https://codeload.github.com/stjudecloud/msgenctl/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243748052,"owners_count":20341627,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":"2024-11-21T12:15:33.851Z","updated_at":"2025-03-15T15:25:37.568Z","avatar_url":"https://github.com/stjudecloud.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"# msgenctl\n\n[![CI status](https://github.com/stjudecloud/msgenctl/workflows/CI/badge.svg)](https://github.com/stjudecloud/msgenctl/actions/workflows/ci.yml)\n\n**msgenctl** is a CLI to manage [Microsoft Genomics] workflows.\n\n[Microsoft Genomics]: https://azure.microsoft.com/en-us/services/genomics/\n\n## Install\n\n[Precompiled binaries] of msgenctl are built for Linux distributions\n(`linux/amd64`), macOS (`darwin/amd64`), and Windows (`windows/amd64`).\n\nAlternatively, it can be compiled from source.\n\n```bash\n$ git clone https://github.com/stjudecloud/msgenctl\n$ cd msgenctl\n$ go build\n$ ./msgenctl --help\n```\n\n[Precompiled binaries]: https://github.com/stjudecloud/msgenctl/releases\n\n## Usage\n\n```\nQuery and send commands to Microsoft Genomics\n\nUsage:\n  msgenctl [command]\n\nAvailable Commands:\n  cancel      cancels a running workflow\n  completion  generate the autocompletion script for the specified shell\n  status      prints the status a workflow or all workflows\n  submit      submits a new workflow\n  wait        polls until the completion of a workflow\n\nFlags:\n      --access-key string   Microsoft Genomics API access key\n      --base-url string     Microsoft Genomics API base URL\n  -h, --help                help for msgenctl\n  -v, --version             version for msgenctl\n\nUse \"msgenctl [command] --help\" for more information about a command.\n```\n\n### Examples\n\n#### Submit a workflow\n\n```sh\nmsgenctl submit \\\n    --base-url $MSGEN_BASE_URL \\\n    --access-key $MSGEN_ACCESS_KEY \\\n    --process-name snapgatk \\\n    --process-args R=hg38m1x \\\n    --description sample \\\n    --input-storage-connection-string \"$MSGEN_STORAGE_CONNECTION_STRING\" \\\n    --input-storage-container-name $MSGEN_STORAGE_CONTAINER_NAME \\\n    --input-blob-name sample.bam \\\n    --output-storage-connection-string \"$MSGEN_STORAGE_CONNECTION_STRING\" \\\n    --output-storage-container-name $MSGEN_STORAGE_CONTAINER_NAME\n```\n\n#### Show the status of a workflow\n\n```sh\nmsgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY \u003cworkflow-id\u003e\n```\n\n#### Show the statuses of all workflows\n\n```sh\nmsgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY\n```\n\n#### Wait until a workflow completes\n\n```sh\nmsgenctl wait --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY \u003cworkflow-id\u003e\n```\n\n#### Cancel a workflow\n\n```sh\nmsgenctl cancel --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY \u003cworkflow-id\u003e\n```\n\n## Limitations\n\n  * Input (`--input-blob-name`) is expected to be a single BAM blob. A SAS is\n    automatically generated for it.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fmsgenctl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstjudecloud%2Fmsgenctl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fmsgenctl/lists"}