planemo.galaxy package¶
Subpackages¶
Submodules¶
planemo.galaxy.activity module¶
Module provides generic interface to running Galaxy tools and workflows.
planemo.galaxy.api module¶
A high-level interface to local Galaxy instances using bioblend.
planemo.galaxy.config module¶
Abstractions for setting up a Galaxy instance.
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.
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.
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planemo.galaxy.profiles.
delete_profile
(ctx, profile_name, **kwds)[source]¶ Delete profile with the specified name.
planemo.galaxy.run module¶
Utilities for calling Galaxy scripts.
planemo.galaxy.serve module¶
Abstractions for serving out development Galaxy servers.
planemo.galaxy.workflows module¶
Utilities for Galaxy workflows.
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)¶