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def get_install_repository_manager(options):
"""
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(
def main():
"""
This script uses bioblend to trigger dependencies installations for the provided tools
"""
args = _parser().parse_args()
gi = get_galaxy_connection(args)
tool_client = ToolClient(gi)
if args.verbose:
log.basicConfig(level=log.DEBUG)
if args.tool:
for tool_conf_path in args.tool: # type: str
_, ext = os.path.splitext(tool_conf_path)
if ext == '.xml':
log.info("tool_conf xml found, parsing..")
# install all
root = ET.ElementTree(file=tool_conf_path).getroot()
if root.tag == "toolbox":
# Install all from tool_conf
tool_path = root.get('tool_path', '')
tool_path = tool_path.replace('${tool_conf_dir}', os.path.abspath(os.path.dirname(tool_conf_path)))