Home

Welcome to the ICAv2 CLI Plugins Home Page

Installation

Please head to the installation page for instructions on how to install this plugin.

For information on icav2 context handling, please visit the context page.

This includes:

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: