planemo.galaxy package¶

Subpackages¶

planemo.galaxy.test package

Submodules¶

planemo.galaxy.activity module¶

Module provides generic interface to running Galaxy tools and workflows.

planemo.galaxy.activity.execute(ctx, config, runnable, job_path, **kwds)[source]¶: Execute a Galaxy activity.

planemo.galaxy.api module¶

A high-level interface to local Galaxy instances using bioblend.

planemo.galaxy.api.gi(port=None, url=None, key=None)[source]¶: Return a bioblend GalaxyInstance for Galaxy on this port.

planemo.galaxy.api.user_api_key(admin_gi)[source]¶: Use an admin authenticated account to generate a user API key.

planemo.galaxy.config module¶

Abstractions for setting up a Galaxy instance.

planemo.galaxy.config.galaxy_config(ctx, runnables, **kwds)[source]¶: Set up a GalaxyConfig in an auto-cleaned context.

planemo.galaxy.distro_tools module¶

planemo.galaxy.ephemeris_sleep module¶

Utility to do a blocking sleep until a Galaxy instance is responsive. This is useful in docker images, in RUN steps, where one needs to wait for a currently starting Galaxy to be alive, before API requests can be made successfully. The script functions by making repeated requests to http(s)://fqdn/api/version, an API which requires no authentication to access.

class planemo.galaxy.ephemeris_sleep.SleepCondition[source]¶

Bases: object

cancel()[source]¶

planemo.galaxy.ephemeris_sleep.main()[source]¶: Main function

planemo.galaxy.ephemeris_sleep.sleep(galaxy_url, verbose=False, timeout=0, sleep_condition=None)[source]¶

planemo.galaxy.profiles module¶

This modules describes the abstraction of a Galaxy profile.

This is a workspace with a specific default configuration and shed tool setup. It is meant to be used with various serve commands.

planemo.galaxy.profiles.create_profile(ctx, profile_name, **kwds)[source]¶: Create a profile with the specified name.

planemo.galaxy.profiles.delete_profile(ctx, profile_name, **kwds)[source]¶: Delete profile with the specified name.

planemo.galaxy.profiles.ensure_profile(ctx, profile_name, **kwds)[source]¶: Ensure a Galaxy profile exists and return profile defaults.

planemo.galaxy.profiles.list_profiles(ctx, **kwds)[source]¶: Return a list of current profile names.

planemo.galaxy.run module¶

Utilities for calling Galaxy scripts.

planemo.galaxy.run.setup_venv(ctx, kwds)[source]¶

planemo.galaxy.run.run_galaxy_command(ctx, command, env, action)[source]¶: Run Galaxy command with informative verbose logging.

planemo.galaxy.run.setup_common_startup_args()[source]¶

planemo.galaxy.serve module¶

Abstractions for serving out development Galaxy servers.

planemo.galaxy.serve.serve(ctx, runnables=None, **kwds)[source]¶

planemo.galaxy.serve.serve_daemon(ctx, runnables=None, **kwds)[source]¶: Serve a daemonized Galaxy instance with artifacts defined by paths.

planemo.galaxy.serve.shed_serve(ctx, install_args_list, **kwds)[source]¶: Serve a daemon instance of Galaxy with specified repositories installed.

planemo.galaxy.workflows module¶

Utilities for Galaxy workflows.

planemo.galaxy.workflows.import_workflow(path, admin_gi, user_gi, from_path=False)[source]¶: Import a workflow path to specified Galaxy instance.

planemo.galaxy.workflows.describe_outputs(runnable, gi=None)[source]¶: Return a list of WorkflowOutput objects for target workflow.

Module contents¶

Entry-point for Galaxy specific functionality in Planemo.

planemo.galaxy.galaxy_config(ctx, runnables, **kwds)[source]¶: Set up a GalaxyConfig in an auto-cleaned context.

planemo.galaxy.setup_venv(ctx, kwds)[source]¶

planemo.galaxy.run_galaxy_command(ctx, command, env, action)[source]¶: Run Galaxy command with informative verbose logging.

planemo.galaxy.galaxy_serve(ctx, runnables=None, **kwds)¶

planemo.galaxy.shed_serve(ctx, install_args_list, **kwds)[source]¶: Serve a daemon instance of Galaxy with specified repositories installed.