planemo.galaxy 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.
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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.
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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]
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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.
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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.
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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]
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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.
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planemo.galaxy.serve.
serve
(ctx, runnables=None, **kwds)[source]
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planemo.galaxy.serve.
serve_daemon
(ctx, runnables=None, **kwds)[source]
Serve a daemonized Galaxy instance with artifacts defined by paths.
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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.
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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.
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planemo.galaxy.
galaxy_serve
(ctx, runnables=None, **kwds)
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planemo.galaxy.
shed_serve
(ctx, install_args_list, **kwds)[source]
Serve a daemon instance of Galaxy with specified repositories installed.