msgenctl is a CLI to manage Microsoft Genomics workflows.
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 --helpQuery 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.
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_NAMEmsgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY <workflow-id>msgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEYmsgenctl wait --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY <workflow-id>msgenctl cancel --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY <workflow-id>- Input (
--input-blob-name) is expected to be a single BAM blob. A SAS is automatically generated for it.