@galaxyproject/galaxy-cli

Galaxy agent operations on the command line. One subcommand per operation -- histories, datasets, tools, workflows, and the IWC catalog -- with table / JSON output and meaningful exit codes. Built on @galaxyproject/galaxy-ops.

Install

npm install -g @galaxyproject/galaxy-cli   # provides the `galaxy-cli` command
# or run without installing:
npx @galaxyproject/galaxy-cli --help

Requires Node.js >=22.19.

Usage

Set your Galaxy connection, then run a command:

export GALAXY_URL=https://usegalaxy.org/
export GALAXY_API_KEY=your-api-key

galaxy-cli get_user
galaxy-cli --format json get_histories --name rnaseq
galaxy-cli get_workflow_input_template <workflowId>
galaxy-cli invoke_workflow <workflowId> --inputs @inputs.json --history-name "WF run"

Credentials resolve from (first match wins): --url/--api-key flags, the GALAXY_URL/GALAXY_API_KEY environment variables, a .env file in the current directory, or a planemo profile (--profile <name>). Output is a table by default; --format json prints the full result envelope for scripting. Exit codes follow sysexits.h conventions (e.g. 77 for auth failures).

Run galaxy-cli --help, or galaxy-cli <command> --help, for the full list of commands and their arguments.

Documentation

See the galaxy-agent-tools workspace README for the full operation list, output formats, and exit-code reference.

License

MIT