planemo.galaxy package

Submodules

planemo.galaxy.activity module

Module provides generic interface to running Galaxy tools and workflows.

planemo.galaxy.activity.execute(ctx: PlanemoCliContext, config: BaseGalaxyConfig, runnable: planemo.runnable.Runnable, job_path: str, **kwds) → planemo.runnable.RunResponse[source]

Execute a Galaxy activity.

planemo.galaxy.api module

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

planemo.galaxy.api.gi(port: Optional[int] = None, url: Optional[str] = None, key: Optional[str] = None) → bioblend.galaxy.GalaxyInstance[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: Dict[str, Any], config: Optional[LocalGalaxyConfig] = None)[source]
planemo.galaxy.run.run_galaxy_command(ctx, command, env, action)[source]

Run Galaxy command with informative verbose logging.

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.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: Dict[str, Any], config: Optional[LocalGalaxyConfig] = None)[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)