https://github.com/stjudecloud/msgenctl
CLI to manage Microsoft Genomics workflows
https://github.com/stjudecloud/msgenctl
Last synced: over 1 year ago
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CLI to manage Microsoft Genomics workflows
- Host: GitHub
- URL: https://github.com/stjudecloud/msgenctl
- Owner: stjudecloud
- License: mit
- Created: 2021-08-19T16:15:28.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-10-28T19:38:31.000Z (over 1 year ago)
- Last Synced: 2025-01-22T05:28:48.550Z (over 1 year ago)
- Language: Go
- Size: 150 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.txt
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README
# msgenctl
[](https://github.com/stjudecloud/msgenctl/actions/workflows/ci.yml)
**msgenctl** is a CLI to manage [Microsoft Genomics] workflows.
[Microsoft Genomics]: https://azure.microsoft.com/en-us/services/genomics/
## 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.
```bash
$ git clone https://github.com/stjudecloud/msgenctl
$ cd msgenctl
$ go build
$ ./msgenctl --help
```
[Precompiled binaries]: https://github.com/stjudecloud/msgenctl/releases
## 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
```sh
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
```sh
msgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY
```
#### Show the statuses of all workflows
```sh
msgenctl status --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY
```
#### Wait until a workflow completes
```sh
msgenctl wait --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY
```
#### Cancel a workflow
```sh
msgenctl cancel --base-url $MSGEN_BASE_URL --access-key $MSGEN_ACCESS_KEY
```
## Limitations
* Input (`--input-blob-name`) is expected to be a single BAM blob. A SAS is
automatically generated for it.