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Alexis Lucattini edited this page Oct 29, 2026 · 16 revisions

Welcome to the ICAv2 CLI Plugins Home Page

Installation

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

Configuration

The CLI uses an AWS CLI-style, two-level tenant + profile configuration stored in ~/.icav2-cli-plugins/config. Credentials live in a tenant section (shared across that tenant's projects, with a user-scoped token) and each project context lives in a profile that points at a tenant. See the Configuration page for full details.

Quick start after installation:

# Configure the tenant once (credentials)
icav2 configure set-tenant umccr

# Configure a profile per project (points at the tenant; profile name required)
icav2 configure set-profile default
icav2 configure set-profile production

# List all profiles
icav2 configure list

# Export a profile's context into the current shell
eval "$(icav2 configure export production)"

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Context Handling

For information on setting and switching project contexts, please visit the context page.

Note: icav2 projects enter is deprecated and no longer functional. Credentials, the ICA server, and the project context are managed with the two-level tenant/profile configuration (icav2 configure set-tenant and icav2 configure set-profile). See the Configuration page.

This includes:

  • Selecting a profile with the --profile flag or the ICAV2_PROFILE env var
    • For setting or switching project contexts per command or per terminal

Project Data

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

Project Pipelines

For information on plugins for icav2 projectpipelines, please visit the projectpipeline_page

This includes:

  • icav2 projectpipeline create-cwl-pipeline-from-zip
    • Given a zip file, create a cwl workflow in the current project context
  • icav2 projectpipeline create-wes-input-template
    • Create a WES input template for a given pipeline id or pipeline code
  • icav2 projectpipeline start-wes
    • Start a pipeline analysis from an input template

Project Analyses

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

Bundles

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

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