Further fix docker paths on mac

Author: ThomasHickman

cwltool/docker.py

@@ -257,7 +257,7 @@ def add_volumes(self, pathmapper, runtime, secret_store=None):
                         f.write(contents.encode("utf-8"))
                     runtime.append(u"--volume=%s:%s:rw" % (
                         docker_windows_path_adjust(os.path.realpath(createtmp)),
-                        docker_windows_path_adjust(os.path.realpath(vol.target))))
+                        vol.target))
 
     def create_runtime(self, env, runtimeContext):
         # type: (MutableMapping[Text, Text], RuntimeContext) -> List
@@ -309,7 +309,7 @@ def create_runtime(self, env, runtimeContext):
         if runtimeContext.rm_container:
             runtime.append(u"--rm")
 
-        runtime.append(u"--env=TMPDIR=%s" % self.builder.tmpdir)
+        runtime.append(u"--env=TMPDIR=/tmp")
 
         # spec currently says "HOME must be set to the designated output
         # directory." but spec might change to designated temp directory.

cwltool/process.py

@@ -623,16 +623,12 @@ def _init_job(self, joborder, runtimeContext):
                         dockerReq.get("dockerOutputDirectory").startswith('/'):
                     outdir = dockerReq.get("dockerOutputDirectory")
                 else:
-                    outdir = fs_access.docker_compatible_realpath(
-                        dockerReq.get("dockerOutputDirectory") or
-                        runtimeContext.docker_outdir or "/var/spool/cwl")
+                    outdir = dockerReq.get("dockerOutputDirectory") or \
+                        runtimeContext.docker_outdir or "/var/spool/cwl"
             elif defaultDocker:
-                outdir = fs_access.docker_compatible_realpath(
-                    runtimeContext.docker_outdir or "/var/spool/cwl")
-            tmpdir = fs_access.docker_compatible_realpath(
-                runtimeContext.docker_tmpdir or "/tmp")
-            stagedir = fs_access.docker_compatible_realpath(
-                runtimeContext.docker_stagedir or "/var/lib/cwl")
+                outdir = runtimeContext.docker_outdir or "/var/spool/cwl"
+            tmpdir = runtimeContext.docker_tmpdir or "/tmp"
+            stagedir = runtimeContext.docker_stagedir or "/var/lib/cwl"
         else:
             outdir = fs_access.realpath(runtimeContext.outdir or
                 tempfile.mkdtemp(prefix=getdefault(runtimeContext.tmp_outdir_prefix,