smaht_pipeline_utils
This is the entry point for a collection of utilities available as commands:
Usage:
smaht_pipeline_utils [COMMAND] [ARGS]
pipeline_deploy
Utility to automatically deploy pipeline’s components from a target repository. It is possible to specify multiple target repositories to deploy multiple pipelines at the same time.
Usage:
smaht_pipeline_utils pipeline_deploy --ff-env FF_ENV --repos REPO [REPO ...] [OPTIONAL ARGS]
Arguments:
Argument |
Definition |
|---|---|
--ff-env |
Environment to use for deployment |
--repos |
List of directories for the repositories to deploy, each repository must follow the expected structure (see docs) |
Optional Arguments:
Argument |
Definition |
|---|---|
--builder |
Builder to use to deploy Docker containers to AWS ECR through AWS CodeBuild [<ff-env>-pipeline-builder] |
--branch |
Branch to use to deploy Docker containers to AWS ECR through AWS CodeBuild [main] |
--local-build |
Trigger a local build for Docker containers instead of using AWS CodeBuild |
--keydicts-json |
Path to file with keys for portal auth in JSON format [~/.cgap-keys.json] |
--wfl-bucket |
Bucket to use for upload of Workflow Description files (CWL or WDL) |
--account |
AWS account to use for deployment |
--region |
AWS account region to use for deployment |
--consortia |
List of consortia to use for deployment [smaht] |
--submission-centers |
List of centers to use for deployment [smaht_dac] |
--post-software |
DEPLOY | UPDATE Software objects (.yaml or .yml) |
--post-file-format |
DEPLOY | UPDATE File Format objects (.yaml or .yml) |
--post-file-reference |
DEPLOY | UPDATE File Reference objects (.yaml or .yml) |
--post-workflow |
DEPLOY | UPDATE Workflow objects (.yaml or .yml) |
--post-metaworkflow |
DEPLOY | UPDATE Pipeline objects (.yaml or .yml) |
--post-wfl |
Upload Workflow Description files (.cwl or .wdl) |
--post-ecr |
Build Docker container images and push to AWS ECR. By default will use AWS CodeBuild unless --local-build flag is set |
--debug |
Turn off DEPLOY | UPDATE action |
--verbose |
Print the JSON structure created for the objects |
--validate |
Validate YAML objects against schemas. Turn off DEPLOY | UPDATE action |
--sentieon-server |
Address for Sentieon license server |