Fix "File is not accessible error".

This error was due to directory being extracted in /tmp, which is not visible by docker.
common-workflow-lab · Mar 4, 2019 · b1fe4bf · b1fe4bf
1 parent 3928f21
commit b1fe4bf
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -2470,11 +2470,13 @@ def exec_before_job(self, app, inp_data, out_data, param_dict=None):
 
                     assert os.path.exists(tar_file_location), tar_file_location
 
-                    tmp_dir = os.path.join('/tmp', str(uuid.uuid4()))
+                    tmp_dir = os.path.join(local_working_directory, 'direx', str(uuid.uuid4())) # direx for "DIR EXtract"                                                                                                         
                     directory_location = os.path.join(tmp_dir, directory_name)
 
                     os.makedirs(tmp_dir)
 
+                    assert os.path.exists(tmp_dir), tmp_dir                                                                                                                                                                       
+
                     bkp_cwd = os.getcwd(); os.chdir(tmp_dir)
                     tar = tarfile.open(tar_file_location); tar.extractall(); tar.close()
                     os.chdir(bkp_cwd)