9309: Look for fpm-info in backports/$PACKAGE_NAME.

[arvados.git] / crunch_scripts / cwl-runner

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 5e7982cec5ec8c34f0c203e5e921e49c00e9845f..c786fc10b1715e1c5912e13ee98011aa94dceab3 100755 (executable)
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -20,6 +20,7 @@ import json
 import argparse
 from arvados.api import OrderedJsonModel
 from cwltool.process import adjustFiles
+from cwltool.load_tool import load_tool
 
 # Print package versions
 logging.info(cwltool.main.versionstring())
@@ -48,7 +49,7 @@ try:
 
     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
 
-    t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
+    t = load_tool(job_order_object, runner.arvMakeTool)
 
     args = argparse.Namespace()
     args.project_uuid = arvados.current_job()["owner_uuid"]
@@ -57,6 +58,7 @@ try:
     args.debug = True
     args.quiet = False
     args.ignore_docker_for_reuse = False
+    args.basedir = os.getcwd()
     args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
     outputObj = runner.arvExecutor(t, job_order_object, **vars(args))