def cli(ctx, paths, **kwds):
"""Launch Galaxy with Tool Shed dependencies.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and serve a Galaxy instances that can be
logged into and explored interactively.
"""
kwds['galaxy_skip_client_build'] = False
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
with shed_serve(ctx, install_args_list, **kwds) as config:
io.info("Galaxy running with tools installed at %s" % config.galaxy_url)
sleep_for_serve()
def cli(ctx, workflow_path, output=None, force=False, **kwds):
"""Open a synchronized Galaxy workflow editor.
"""
assert is_galaxy_engine(**kwds)
kwds["workflows_from_path"] = True
runnable = for_path(workflow_path)
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id(workflow_path)
url = "%s/workflow/editor?id=%s" % (config.galaxy_url, workflow_id)
click.launch(url)
sleep_for_serve()
def cli(ctx, paths, **kwds):
"""Launch Galaxy with Tool Shed dependencies.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and serve a Galaxy instances that can be
logged into and explored interactively.
"""
kwds['galaxy_skip_client_build'] = False
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
with shed_serve(ctx, install_args_list, **kwds) as config:
io.info("Galaxy running with tools installed at %s" %
config.galaxy_url)
sleep_for_serve()
def cli(ctx, workflow_identifier, output=None, force=False, **kwds):
"""Open a synchronized Galaxy workflow editor.
"""
assert is_galaxy_engine(**kwds)
runnable = for_runnable_identifier(ctx, workflow_identifier, kwds.get("profile"))
kwds["workflows_from_path"] = True
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id_for_runnable(runnable)
url = "%s/workflow/editor?id=%s" % (config.galaxy_url, workflow_id)
click.launch(url)
if kwds["engine"] != "external_galaxy":
sleep_for_serve()
def cli(ctx, workflow_identifier, output=None, force=False, **kwds):
"""Open a synchronized Galaxy workflow editor.
"""
assert is_galaxy_engine(**kwds)
workflow_identifier = translate_alias(ctx, workflow_identifier,
kwds.get('profile'))
if os.path.exists(workflow_identifier):
runnable = for_path(workflow_identifier)
else: # assume galaxy workflow id
runnable = for_id(workflow_identifier)
kwds["workflows_from_path"] = True
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id_for_runnable(runnable)
url = "%s/workflow/editor?id=%s" % (config.galaxy_url, workflow_id)
click.launch(url)
if kwds["engine"] != "external_galaxy":
sleep_for_serve()