Merge branch 'master' into disable_user

Author: mr-c

cwltool/job.py

@@ -158,9 +158,9 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
                     with open(createtmp, "w") as f:
                         f.write(vol.resolved.encode("utf-8"))
                     runtime.append(u"--volume=%s:%s:ro" % (createtmp, vol.target))
-            runtime.append(u"--volume=%s:%s:rw" % (os.path.realpath(self.outdir), "/var/spool/cwl"))
+            runtime.append(u"--volume=%s:%s:rw" % (os.path.realpath(self.outdir), self.builder.outdir))
             runtime.append(u"--volume=%s:%s:rw" % (os.path.realpath(self.tmpdir), "/tmp"))
-            runtime.append(u"--workdir=%s" % ("/var/spool/cwl"))
+            runtime.append(u"--workdir=%s" % (self.builder.outdir))
             runtime.append("--read-only=true")
 
             if kwargs.get("custom_net", None) is not None:
@@ -184,7 +184,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
             # spec currently says "HOME must be set to the designated output
             # directory." but spec might change to designated temp directory.
             # runtime.append("--env=HOME=/tmp")
-            runtime.append("--env=HOME=/var/spool/cwl")
+            runtime.append("--env=HOME=%s" % self.builder.outdir)
 
             for t,v in self.environment.items():
                 runtime.append(u"--env=%s=%s" % (t, v))

cwltool/process.py

@@ -460,7 +460,7 @@ def _init_job(self, joborder, **kwargs):
         builder.fs_access = builder.make_fs_access(kwargs["basedir"])
 
         if dockerReq and kwargs.get("use_container"):
-            builder.outdir = builder.fs_access.realpath(kwargs.get("docker_outdir") or "/var/spool/cwl")
+            builder.outdir = builder.fs_access.realpath(dockerReq.get("dockerOutputDirectory") or kwargs.get("docker_outdir") or "/var/spool/cwl")
             builder.tmpdir = builder.fs_access.realpath(kwargs.get("docker_tmpdir") or "/tmp")
             builder.stagedir = builder.fs_access.realpath(kwargs.get("docker_stagedir") or "/var/lib/cwl")
         else: