Merge pull request #814 from wtsi-hgi/fix-812

Fix #812 (incorrect mac paths)

Author: mr-c

cwltool/docker.py

@@ -256,8 +256,8 @@ def add_volumes(self, pathmapper, runtime, secret_store=None):
                     with os.fdopen(fd, "wb") as f:
                         f.write(contents.encode("utf-8"))
                     runtime.append(u"--volume=%s:%s:rw" % (
-                        docker_windows_path_adjust(createtmp),
-                        docker_windows_path_adjust(vol.target)))
+                        docker_windows_path_adjust(os.path.realpath(createtmp)),
+                        vol.target))
 
     def create_runtime(self, env, runtimeContext):
         # type: (MutableMapping[Text, Text], RuntimeContext) -> List

cwltool/process.py

@@ -609,16 +609,12 @@ 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,