Merge branch 'master' into unicode_literal_usage

Author: manu-chroma

cwltool/main.py

@@ -35,7 +35,7 @@
                       relocateOutputs, scandeps, shortname, use_custom_schema,
                       use_standard_schema)
 from .resolver import ga4gh_tool_registries, tool_resolver
-from .software_requirements import DependenciesConfiguration, get_container_from_software_requirements
+from .software_requirements import DependenciesConfiguration, get_container_from_software_requirements, SOFTWARE_REQUIREMENTS_ENABLED
 from .stdfsaccess import StdFsAccess
 from .update import ALLUPDATES, UPDATES
 
@@ -155,14 +155,21 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
 
-    # help="Dependency resolver configuration file describing how to adapt 'SoftwareRequirement' packages to current system."
-    parser.add_argument("--beta-dependency-resolvers-configuration", default=None, help=argparse.SUPPRESS)
-    # help="Defaut root directory used by dependency resolvers configuration."
-    parser.add_argument("--beta-dependencies-directory", default=None, help=argparse.SUPPRESS)
-    # help="Use biocontainers for tools without an explicitly annotated Docker container."
-    parser.add_argument("--beta-use-biocontainers", default=None, help=argparse.SUPPRESS, action="store_true")
-    # help="Short cut to use Conda to resolve 'SoftwareRequirement' packages."
-    parser.add_argument("--beta-conda-dependencies", default=None, help=argparse.SUPPRESS, action="store_true")
+    dependency_resolvers_configuration_help = argparse.SUPPRESS
+    dependencies_directory_help = argparse.SUPPRESS
+    use_biocontainers_help = argparse.SUPPRESS
+    conda_dependencies = argparse.SUPPRESS
+
+    if SOFTWARE_REQUIREMENTS_ENABLED:
+        dependency_resolvers_configuration_help = "Dependency resolver configuration file describing how to adapt 'SoftwareRequirement' packages to current system."
+        dependencies_directory_help = "Defaut root directory used by dependency resolvers configuration."
+        use_biocontainers_help = "Use biocontainers for tools without an explicitly annotated Docker container."
+        conda_dependencies = "Short cut to use Conda to resolve 'SoftwareRequirement' packages."
+
+    parser.add_argument("--beta-dependency-resolvers-configuration", default=None, help=dependency_resolvers_configuration_help)
+    parser.add_argument("--beta-dependencies-directory", default=None, help=dependencies_directory_help)
+    parser.add_argument("--beta-use-biocontainers", default=None, help=use_biocontainers_help, action="store_true")
+    parser.add_argument("--beta-conda-dependencies", default=None, help=conda_dependencies, action="store_true")
 
     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
 

cwltool/software_requirements.py

@@ -22,6 +22,7 @@
 
 from .utils import get_feature
 
+SOFTWARE_REQUIREMENTS_ENABLED = deps is not None
 
 COMMAND_WITH_DEPENDENCIES_TEMPLATE = string.Template("""#!/bin/bash
 $handle_dependencies
@@ -60,8 +61,7 @@ def config_dict(self):
 
     def build_job_script(self, builder, command):
         # type: (Any, List[str]) -> Text
-        if deps is None:
-            raise Exception("galaxy-lib not found")
+        ensure_galaxy_lib_available()
         tool_dependency_manager = deps.build_dependency_manager(self)  # type: deps.DependencyManager
         dependencies = get_dependencies(builder)
         handle_dependencies = ""  # str
@@ -99,11 +99,8 @@ def get_dependencies(builder):
 
 def get_container_from_software_requirements(args, builder):
     if args.beta_use_biocontainers:
-        try:
-            from galaxy.tools.deps.containers import ContainerRegistry, AppInfo, ToolInfo, DOCKER_CONTAINER_TYPE
-        except ImportError:
-            raise Exception("Optional requirement galaxy-lib not found, it is required for this configuration.")
-
+        ensure_galaxy_lib_available()
+        from galaxy.tools.deps.containers import ContainerRegistry, AppInfo, ToolInfo, DOCKER_CONTAINER_TYPE
         app_info = AppInfo(
             involucro_auto_init=True,
             enable_beta_mulled_containers=True,
@@ -117,3 +114,9 @@ def get_container_from_software_requirements(args, builder):
             return container_description.identifier
 
     return None
+
+
+def ensure_galaxy_lib_available():
+    # type: () -> None
+    if not SOFTWARE_REQUIREMENTS_ENABLED:
+        raise Exception("Optional Python library galaxy-lib not available, it is required for this configuration.")