msgenctl

msgenctl is a CLI to manage Microsoft Genomics workflows.

Install

Precompiled binaries of msgenctl are built for Linux distributions (linux/amd64), macOS (darwin/amd64), and Windows (windows/amd64).

Alternatively, it can be compiled from source.

$ git clone https://github.com/stjudecloud/msgenctl
$ cd msgenctl
$ go build
$ ./msgenctl --help

Usage

Query and send commands to Microsoft Genomics

Usage:
  msgenctl [command]

Available Commands:
  cancel      cancels a running workflow
  completion  generate the autocompletion script for the specified shell
  status      prints the status a workflow or all workflows
  submit      submits a new workflow
  wait        polls until the completion of a workflow

Flags:
      --access-key string   Microsoft Genomics API access key
      --base-url string     Microsoft Genomics API base URL
  -h, --help                help for msgenctl
  -v, --version             version for msgenctl

Use "msgenctl [command] --help" for more information about a command.

Examples

Submit a workflow

msgenctl submit \
    --base-url $MSGEN_BASE_URL \
    --access-key $MSGEN_ACCESS_KEY \
    --process-name snapgatk \
    --process-args R=hg38m1x \
    --description sample \
    --input-storage-connection-string "$MSGEN_STORAGE_CONNECTION_STRING" \
    --input-storage-container-name $MSGEN_STORAGE_CONTAINER_NAME \
    --input-blob-name sample.bam \
    --output-storage-connection-string "$MSGEN_STORAGE_CONNECTION_STRING" \
    --output-storage-container-name $MSGEN_STORAGE_CONTAINER_NAME

Show the status of a workflow

msgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY <workflow-id>

Show the statuses of all workflows

msgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY

Wait until a workflow completes

msgenctl wait --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY <workflow-id>

Cancel a workflow

msgenctl cancel --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY <workflow-id>

Limitations

• Input (--input-blob-name) is expected to be a single BAM blob. A SAS is automatically generated for it.