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"""
Parse the default input file and proceed to install listed tools.
:type options: OptionParser object
:param options: command line arguments parsed by OptionParser
"""
install_tool_dependencies = INSTALL_TOOL_DEPENDENCIES
install_repository_dependencies = INSTALL_REPOSITORY_DEPENDENCIES
install_resolver_dependencies = INSTALL_RESOLVER_DEPENDENCIES
repo_list_file = options.tool_list_file
gi = get_galaxy_connection(options, file=repo_list_file, log=log)
if not gi:
raise Exception('Could not get a galaxy connection')
if repo_list_file:
repository_list = load_yaml_file(repo_list_file) # Input file contents
repositories = repository_list['tools'] # The list of tools to install
install_repository_dependencies = repository_list.get(
'install_repository_dependencies', INSTALL_REPOSITORY_DEPENDENCIES)
install_resolver_dependencies = repository_list.get(
'install_resolver_dependencies', INSTALL_RESOLVER_DEPENDENCIES)
install_tool_dependencies = repository_list.get(
'install_tool_dependencies', INSTALL_TOOL_DEPENDENCIES)
elif options.tool_yaml:
repositories = [yaml.safe_load(options.tool_yaml)]
elif options.action == "update":
get_repository_list = GiToToolYaml(
gi=gi,
skip_tool_panel_section_name=False,
get_data_managers=True
)
repository_list = get_repository_list.tool_list