When running in docker, output dir is now mounted at /var/spool/cwl and TMPDIR

is /tmp.

Author: Peter Amstutz

cwltool/job.py

@@ -63,17 +63,17 @@ def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True,
             for src in self.pathmapper.files():
                 vol = self.pathmapper.mapper(src)
                 runtime.append("--volume=%s:%s:ro" % vol)
-            runtime.append("--volume=%s:%s:rw" % (os.path.abspath(self.outdir), "/tmp/job_output"))
-            runtime.append("--volume=%s:%s:rw" % (os.path.abspath(self.tmpdir), "/tmp/job_tmp"))
-            runtime.append("--workdir=%s" % ("/tmp/job_output"))
+            runtime.append("--volume=%s:%s:rw" % (os.path.abspath(self.outdir), "/var/spool/cwl"))
+            runtime.append("--volume=%s:%s:rw" % (os.path.abspath(self.tmpdir), "/tmp"))
+            runtime.append("--workdir=%s" % ("/var/spool/cwl"))
             runtime.append("--read-only=true")
             euid = docker_vm_uid() or os.geteuid()
             runtime.append("--user=%s" % (euid))
 
             if rm_container:
                 runtime.append("--rm")
 
-            runtime.append("--env=TMPDIR=/tmp/job_tmp")
+            runtime.append("--env=TMPDIR=/tmp")
 
             for t,v in self.environment.items():
                 runtime.append("--env=%s=%s" % (t, v))