def __dependency_manager_for_config(app_config, resolution_config=None):
dm = build_dependency_manager(app_config_dict=app_config,
resolution_config_dict=resolution_config)
if ROUND_TRIP_TEST_DEPENDENCY_MANAGER_SERIALIZATION:
as_dict = dm.to_dict()
dm = build_dependency_manager(resolution_config_dict=as_dict)
return dm
def build_job_script(self, builder: "Builder", command: List[str]) -> str:
ensure_galaxy_lib_available()
resolution_config_dict = {
"use": self.use_tool_dependencies,
"default_base_path": self.tool_dependency_dir,
}
app_config = {
"conda_auto_install": True,
"conda_auto_init": True,
}
tool_dependency_manager = deps.build_dependency_manager(
app_config_dict=app_config,
resolution_config_dict=resolution_config_dict,
conf_file=self.dependency_resolvers_config_file,
) # type: deps.DependencyManager
dependencies = get_dependencies(builder)
handle_dependencies = "" # str
if dependencies:
handle_dependencies = "\n".join(
tool_dependency_manager.dependency_shell_commands(
dependencies, job_directory=builder.tmpdir))
template_kwds = dict(
handle_dependencies=handle_dependencies) # type: Dict[str, str]
job_script = COMMAND_WITH_DEPENDENCIES_TEMPLATE.substitute(
template_kwds)
return job_script
def __dependency_manager_for_base_path(default_base_path, conf_file=None):
dm = DependencyManager(default_base_path=default_base_path,
conf_file=conf_file,
app_config={"conda_auto_init": False})
if ROUND_TRIP_TEST_DEPENDENCY_MANAGER_SERIALIZATION:
as_dict = dm.to_dict()
dm = build_dependency_manager(resolution_config_dict=as_dict)
return dm
def _build_dependency_manager_no_config(kwargs):
"""Simplified variant of build_dependency_manager from galaxy.tool_util.deps.
The canonical factory method requires a full Galaxy configuration object
which we do not have available in this script (an optimization).
"""
configure_logging(kwargs)
base, ext = os.path.splitext(kwargs.get('dependency_resolvers_config_file', 'dependency_resolvers_conf.xml'))
dependency_resolvers_config_file = find_config_file(base, exts=[ext.lstrip('.')])
# FIXME: default is wrong for installed Galaxy
dependency_manager = build_dependency_manager(app_config_dict=kwargs, conf_file=dependency_resolvers_config_file, default_tool_dependency_dir="database/dependencies")
return dependency_manager
def __setup_dependency_manager(self, conf):
default_tool_dependency_dir = "dependencies"
resolvers_config_file = os.path.join(self.config_dir, conf.get("dependency_resolvers_config_file", "dependency_resolvers_conf.xml"))
if build_dependency_manager is not None:
self.dependency_manager = build_dependency_manager(
app_config_dict=conf,
conf_file=resolvers_config_file,
default_tool_dependency_dir=default_tool_dependency_dir
)
else:
dependencies_dir = conf.get("tool_dependency_dir", default_tool_dependency_dir)
conda_config = {k: v for k, v in conf.items() if k.startswith("conda_")}
self.dependency_manager = DependencyManager(dependencies_dir, resolvers_config_file, app_config=conda_config)