#!/usr/bin/python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
import arvados
import subprocess
-import subst
+import crunchutil.subst as subst
import shutil
import os
+import sys
+import time
if len(arvados.current_task()['parameters']) > 0:
p = arvados.current_task()['parameters']
# variant_regions: /path/to/your.bed
''')
+os.unlink("/usr/local/share/bcbio-nextgen/gemini_data")
+os.symlink(arvados.get_job_param_mount("gemini_data"), "/usr/local/share/bcbio-nextgen/gemini_data")
+
os.chdir(arvados.current_task().tmpdir)
rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/freebayes-variant.yaml", "project1",
print("arvados-bcbio-nextgen: start writing output to keep")
done = False
+ api = arvados.api('v1')
while not done:
try:
out = arvados.CollectionWriter()