def for_path(path, temp_path=None):
"""Produce a class:`Runnable` for supplied path."""
runnable_type = None
if os.path.isdir(path):
runnable_type = RunnableType.directory
elif looks_like_a_tool_cwl(path):
runnable_type = RunnableType.cwl_tool
elif looks_like_a_data_manager_xml(path):
runnable_type = RunnableType.galaxy_datamanager
elif looks_like_a_tool_xml(path):
runnable_type = RunnableType.galaxy_tool
elif is_a_yaml_with_class(path, ["GalaxyWorkflow"]):
runnable_type = RunnableType.galaxy_workflow
elif path.endswith(".ga"):
runnable_type = RunnableType.galaxy_workflow
elif looks_like_a_cwl_artifact(path, ["Workflow"]):
runnable_type = RunnableType.cwl_workflow
if runnable_type is None:
error("Unable to determine runnable type for path [%s]" % path)
raise ExitCodeException(EXIT_CODE_UNKNOWN_FILE_TYPE)
if temp_path:
path = _copy_runnable_tree(path, runnable_type, temp_path)
return Runnable(path, runnable_type)
def cli(ctx, paths, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(ctx, **kwds)
if not conda_context.is_conda_installed():
auto_init = kwds.get("conda_auto_init", False)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error("Attempted to install conda and failed.")
else:
failed = False
else:
error("Cannot install conda, failing conda_install.")
else:
error(
"Conda not configured - run planemo conda_init' or pass --conda_auto_init to continue."
)
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
return_codes = []
for conda_target in collect_conda_targets(ctx, paths):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def for_path(path, temp_path=None):
"""Produce a class:`Runnable` for supplied path."""
runnable_type = None
if os.path.isdir(path):
runnable_type = RunnableType.directory
elif looks_like_a_tool_cwl(path):
runnable_type = RunnableType.cwl_tool
elif looks_like_a_data_manager_xml(path):
runnable_type = RunnableType.galaxy_datamanager
elif looks_like_a_tool_xml(path):
runnable_type = RunnableType.galaxy_tool
elif is_a_yaml_with_class(path, ["GalaxyWorkflow"]):
runnable_type = RunnableType.galaxy_workflow
elif path.endswith(".ga"):
runnable_type = RunnableType.galaxy_workflow
elif looks_like_a_cwl_artifact(path, ["Workflow"]):
runnable_type = RunnableType.cwl_workflow
else:
# Check to see if it is a Galaxy workflow with a different extension
try:
with open(path, "r") as f:
as_dict = yaml.safe_load(f)
if as_dict.get("a_galaxy_workflow", False):
runnable_type = RunnableType.galaxy_workflow
except Exception:
pass
if runnable_type is None:
error("Unable to determine runnable type for path [%s]" % path)
raise ExitCodeException(EXIT_CODE_UNKNOWN_FILE_TYPE)
if temp_path:
path = _copy_runnable_tree(path, runnable_type, temp_path)
return Runnable(path, runnable_type)
def build_conda_context(ctx, **kwds):
"""Build a galaxy-lib CondaContext tailored to planemo use.
Using planemo's common command-line/global config options.
"""
condarc_override_default = os.path.join(ctx.workspace, "condarc")
conda_prefix = kwds.get("conda_prefix", None)
use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
ensure_channels = kwds.get("conda_ensure_channels", "")
condarc_override = kwds.get("condarc", condarc_override_default)
use_local = kwds.get("conda_use_local", False)
shell_exec = shell if use_planemo_shell else None
conda_context = conda_util.CondaContext(conda_prefix=conda_prefix,
ensure_channels=ensure_channels,
condarc_override=condarc_override,
use_local=use_local,
shell_exec=shell_exec)
handle_auto_init = kwds.get("handle_auto_init", False)
if handle_auto_init and not conda_context.is_installed():
auto_init = kwds.get("conda_auto_init", True)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error(MESSAGE_ERROR_FAILED_INSTALL)
else:
failed = False
else:
error(MESSAGE_ERROR_CANNOT_INSTALL)
else:
error(MESSAGE_ERROR_NOT_INSTALLING)
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
if handle_auto_init:
conda_context.ensure_conda_build_installed_if_needed()
return conda_context
def exit(self, exit_code):
"""Exit planemo with the supplied exit code."""
self.vlog("Exiting planemo with exit code [%d]" % exit_code)
raise ExitCodeException(exit_code)