ICAv2 CLI Plugins

I'm sorry I couldn't think of a superhero pun for this repository

This plugin contains the following extensions to the icav2 cli.

Much of this is inspired from the ica-ica-lazy repo.

Autocompletion features are courtesy of the app-spec project

Please refer to wiki page for installation and usage.

Features

icav2 bundles extensions

Support for generating and deploying bundles

icav2 bundles init

Initialise a bundle

See more in icav2 bundles init

icav2 bundles get

Get a bundle

See more in icav2_bundles_get

icav2 bundles list

List bundles

See more in icav2_bundles_list

icav2 bundles add-data

Add data to a bundle

See more in icav2_bundles_add_data

icav2 bundles add-pipeline

Add pipeline to a bundle

See more in icav2_bundles_add_pipeline

icav2 bundles release

Release a bundle

See more in icav2_bundles_release

icav2 bundles add-bundle-to-project

Add a released bundle to a project

See more in icav2_bundles_add_to_project

icav2 context handling extensions

icav2 tenants init

Register a tenant with the plugins repository

See more in icav2_context_handling

icav2 tenants list

List available tenants that have been initialised with 'icav2 tenants init'

See more in icav2_context_handling

icav2 tenants enter

Enter a tenant that has been initialised with 'icav2 tenants init'

See more in icav2_context_handling

• Autocompletion ✅

icav2 tenants set-default-project

Set a default project to enter for a given tenant

See more in icav2_context_handling

icav2 tenants set-default-tenant

Set a registered tenant to be the default tenant Replaces api key in $HOME/.icav2/config.yaml

See more in icav2_context_handling

icav2 projects enter

Inspired by ica-context-switcher Enter a project in a terminal without affecting default project or other open terminals

• Autocompletion ✅

See more in icav2_context_handling

icav2 projectdata extensions

icav2 projectdata ls

Inspired by gds-ls
List all files and folders in directory

• Autocompletion: ✅

See more in project data wiki

icav2 projectdata view

Inspired by gds-view
View a file in stdout

• Autocompletion: ✅

See more in project data wiki

icav2 projectdata find

Inspired by gds-find
Mimics the gnutls find command with --maxdepth, --mindepth, --type and --name parameters available

• Autocompletion ✅

See more in project data wiki

icav2 projectdata s3-sync-download

Inspired by gds-sync-download
Sync files from icav2 to local project with an aws s3 sync command

• Autocompletion ✅

See more in project data wiki

icav2 projectdata s3-sync-upload

Inspired by gds-sync-upload
Sync files from local to icav2 with an aws s3 sync command

• Autocompletion ✅

See more in project data wiki

icav2 projectdata create-download-script

Inspired by gds-create-download-script
Create a download script with a list of encoded presigned urls for a given directory.

• Autocompletion ✅

See more in project data wiki

icav2 projectpipelines extensions

icav2 projectpipelines create-workflow-from-zip

Create a pipeline in an icav2 project from a zipped up CWL directory

• Autocompletion ✅

See more in project pipelines wiki

icav2 projectpipelines create-workflow-from-github-release

Create a pipeline in an icav2 project from a GitHub release

• Autocompletion ✅

See more in project pipelines wiki

icav2 projectpipelines create-wes-input-template

Inspired by cwl-ica-create-workflow-submission-template Create a WES input template ready for launch in ICAv2

• Autocompletion ✅

See more in project pipelines wiki

icav2 projectpipelines start-cwl-wes

Launch a CWL Workflow from a wes template

• Autocompletion ✅

See more in project pipelines wiki

icav2 projectpipelines release

Release a projectpipeline from the CLI

• Autocompletion ✅

See more in project pipelines wiki

icav2 projectanalyses extensions

icav2 projectanalyses get-cwl-analysis-input-json

Collect inputjson used by an analyses

• Autocompletion ✅

See more in project analyses wiki

icav2 projectanalyses get-cwl-analysis-output-json

Collect outputjson used by an analyses

• Autocompletion ✅

See more in project analyses wiki

icav2 projectanalyses list-analysis-steps

Inspired by ica-get-tasks-from-workflow-history
Collect all steps in a workflow run, useful for debugging

• Autocompletion ✅

See more in project analyses wiki

icav2 projectanalyses get-analysis-step-logs

Get logs of a step id for a workflow

• Autocompletion ✅

See more in project analyses wiki

icav2 projectanalyses gantt-plot

Generate a gantt chart for a workflow

• Autocompletion ✅

See more in project analyses wiki

Coming soon

icav2 projectanalyses list-cwltool-step-components --step-name

List all available components to view for a cwltool step.

Mines the cwltool stderr debug logs for available components for a given step name

icav2 projectanalyses get-cwltool-step-components --step-name --component-name

View a component for a cwltool step