Cwltool options (#1205)

* Add CWLTOOL_OPTIONS

Author: Peter Amstutz

README.rst

@@ -4,7 +4,7 @@ Common Workflow Language tool description reference implementation
 
 CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Coverage Status| |Downloads|
 
-|CommandLineTool Support| |DockerRequirement Support| |EnvVarRequirement Support| |ExpressionTool Support| 
+|CommandLineTool Support| |DockerRequirement Support| |EnvVarRequirement Support| |ExpressionTool Support|
 |InitialWorkDirRequirement Support| |InlineJavascriptRequirement Support| |MultipleInputRequirement Support| |Core Support|
 |ResourceRequirement Support| |ScatterRequirement Support| |SchemaDefRequirement Support| |ShellCommandequirement Support|
 |StepInputRequirement Support| |SubWorkflowRequirement Support| |Workflow Support|
@@ -145,6 +145,11 @@ the default cwl-runner use::
 
   cwltool [tool-or-workflow-description] [input-job-settings]
 
+You can set cwltool options in the environment with CWLTOOL_OPTIONS,
+these will be inserted at the beginning of the command line::
+
+  export CWLTOOL_OPTIONS="--debug"
+
 Use with boot2docker
 --------------------
 boot2docker runs Docker inside a virtual machine and it only mounts ``Users``

cwltool/main.py

@@ -517,7 +517,10 @@ def main(argsl=None,                   # type: Optional[List[str]]
         if args is None:
             if argsl is None:
                 argsl = sys.argv[1:]
-            args = arg_parser().parse_args(argsl)
+            addl = []  # type: List[str]
+            if "CWLTOOL_OPTIONS" in os.environ:
+                addl = os.environ["CWLTOOL_OPTIONS"].split(" ")
+            args = arg_parser().parse_args(addl+argsl)
             if args.record_container_id:
                 if not args.cidfile_dir:
                     args.cidfile_dir = os.getcwd()

test-requirements.txt

@@ -4,3 +4,4 @@ pytest-mock >= 1.10.0
 pytest-cov
 arcp >= 0.2.0
 rdflib-jsonld >= 0.4.0
+attrs <19.2.0

tests/test_ext.py

@@ -27,6 +27,14 @@ def test_listing_deep():
               get_data('tests/listing-job.yml')]
     assert main(params) == 0
 
+@needs_docker
+def test_cwltool_options():
+    os.environ["CWLTOOL_OPTIONS"] = "--enable-ext"
+    params = [get_data('tests/wf/listing_deep.cwl'),
+              get_data('tests/listing-job.yml')]
+    assert main(params) == 0
+    del os.environ["CWLTOOL_OPTIONS"]
+
 @needs_docker
 def test_listing_shallow():
     # This fails on purpose, because it tries to access listing in a subdirectory