def get_container_from_software_requirements(
use_biocontainers: bool, builder: "HasReqsHints") -> Optional[str]:
if use_biocontainers:
ensure_galaxy_lib_available()
from galaxy.tool_util.deps.containers import (
DOCKER_CONTAINER_TYPE,
ContainerRegistry,
)
from galaxy.tool_util.deps.dependencies import AppInfo, ToolInfo
app_info = AppInfo(
involucro_auto_init=True,
enable_mulled_containers=True,
container_image_cache_path=".",
) # type: AppInfo
container_registry = ContainerRegistry(
app_info) # type: ContainerRegistry
requirements = get_dependencies(builder)
tool_info = ToolInfo(requirements=requirements) # type: ToolInfo
container_description = container_registry.find_best_container_description(
[DOCKER_CONTAINER_TYPE], tool_info)
if container_description:
return container_description.identifier
return None
def _configure_toolbox(self):
if not isinstance(self, BasicSharedApp):
raise Exception("Must inherit from BasicSharedApp")
self.citations_manager = CitationsManager(self)
self.biotools_metadata_source = get_galaxy_biotools_metadata_source(
self.config)
self.dynamic_tools_manager = DynamicToolManager(self)
self._toolbox_lock = threading.RLock()
self.toolbox = tools.ToolBox(self.config.tool_configs,
self.config.tool_path, self)
galaxy_root_dir = os.path.abspath(self.config.root)
file_path = os.path.abspath(self.config.file_path)
app_info = AppInfo(
galaxy_root_dir=galaxy_root_dir,
default_file_path=file_path,
tool_data_path=self.config.tool_data_path,
shed_tool_data_path=self.config.shed_tool_data_path,
outputs_to_working_directory=self.config.
outputs_to_working_directory,
container_image_cache_path=self.config.container_image_cache_path,
library_import_dir=self.config.library_import_dir,
enable_mulled_containers=self.config.enable_mulled_containers,
container_resolvers_config_file=self.config.
container_resolvers_config_file,
container_resolvers_config_dict=self.config.container_resolvers,
involucro_path=self.config.involucro_path,
involucro_auto_init=self.config.involucro_auto_init,
mulled_channels=self.config.mulled_channels,
)
mulled_resolution_cache = None
if self.config.mulled_resolution_cache_type:
cache_opts = {
"cache.type": self.config.mulled_resolution_cache_type,
"cache.data_dir": self.config.mulled_resolution_cache_data_dir,
"cache.lock_dir": self.config.mulled_resolution_cache_lock_dir,
"cache.expire": self.config.mulled_resolution_cache_expire,
}
mulled_resolution_cache = CacheManager(
**parse_cache_config_options(cache_opts)).get_cache(
'mulled_resolution')
self.container_finder = containers.ContainerFinder(
app_info, mulled_resolution_cache=mulled_resolution_cache)
self._set_enabled_container_types()
index_help = getattr(self.config, "index_tool_help", True)
self.toolbox_search = ToolBoxSearch(
self.toolbox,
index_dir=self.config.tool_search_index_dir,
index_help=index_help)