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Alexis Lucattini edited this page Jun 4, 2023
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Welcome to the ICAv2 CLI Plugins Home Page
Please head to the installation page for instructions on how to install this plugin.
- No emoji: Delivered
- 🚅 Next release
- 🚕 Coming soon
- 💼 In progress
For information on icav2 context handling, please visit the context page.
This includes:
- icav2 projects enter
- For switching project contexts within a single terminal
For information on plugins for icav2 projectdata, please visit the projectdata page
This includes:
- icav2 projectdata ls
- For quick non-recursive listing of files / folders in a directory
- icav2 projectdata view
- For quick viewing of a file in a project context without needing to first download the file
- icav2 projectdata s3-sync-download
- For downloading a directory through aws s3 sync
- icav2 projectdata s3-sync-upload
- For uploading a directory through aws s3 sync
- icav2 projectdata create-download-script
For information on plugins for icav2 projectpipelines, please visit the projectpipeline_page
This includes:
- icav2 projectpipeline create-cwl-workflow-from-zip
- Given a zip file, create a cwl workflow in the current project context
- icav2 projectpipeline create-cwl-wes-input-template
- Create a CWL WES input template for a given pipeline id or pipeline code
- icav2 projectpipeline start-cwl-wes
- Start a pipeline analysis from an input template
For information on plugins for icav2 projectanalyses, please visit the projectanalyses_page
This includes:
- icav2 projectanalyses get-cwl-analysis-input-json
- Get the input json given an analysis id
- icav2 projectanalyses get-cwl-analysis-output-json
- Get the output json given an analysis id
- icav2 projectanalyses list-analysis-steps
- List the analysis steps for a running, complete or failed pipeline analysis
- icav2 projectanalyses get-analysis-step-logs
- Get the stdout or stderr given an analysis id and analysis step
- icav2 projectanalyses gantt-plot
- Show a gantt plot of an analysis over time
For information on plugins for icav2 bundles please visit the bundles_page
This includes:
- icav2 bundles init
- Initialise a bundle
- icav2 bundles get
- Get a bundle
- icav2 bundles list
- List bundles
- icav2 bundles add-data
- Add data to a bundle
- icav2 bundles add-pipeline
- Add pipeline to a bundle
- icav2 bundles release
- Release a bundle
- icav2 bundles add-bundle-to-project
- Add a released bundle to a project