Enable Galaxy outputs_to_working_directory by default (#1199)

bernt-matthias · web-flow · commit 27c256b3cf64 · 2022-05-16T15:54:14.000+01:00
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -484,6 +484,7 @@ def config_join(*args):
                 migrated_tools_config=empty_tool_conf,
                 test_data_dir=test_data_dir,  # TODO: make gx respect this
                 shed_data_manager_config_file=shed_data_manager_config_file,
+                outputs_to_working_directory="True",  # this makes Galaxy's files dir RO for dockerized testing
             )
         )
         _handle_container_resolution(ctx, kwds, properties)
@@ -500,7 +501,6 @@ def config_join(*args):
         # sanitize_all_html = True
         # serve_xss_vulnerable_mimetypes = False
         # track_jobs_in_database = None
-        # outputs_to_working_directory = False
         # retry_job_output_collection = 0
 
         env = _build_env_for_galaxy(properties, template_args)

Original file line number	Diff line number	Diff line change
`@@ -484,6 +484,7 @@ def config_join(*args):`
`484`	`484`	`migrated_tools_config=empty_tool_conf,`
`485`	`485`	`test_data_dir=test_data_dir, # TODO: make gx respect this`
`486`	`486`	`shed_data_manager_config_file=shed_data_manager_config_file,`
	`487`	`+ outputs_to_working_directory="True", # this makes Galaxy's files dir RO for dockerized testing`
`487`	`488`	`)`
`488`	`489`	`)`
`489`	`490`	`_handle_container_resolution(ctx, kwds, properties)`
`@@ -500,7 +501,6 @@ def config_join(*args):`
`500`	`501`	`# sanitize_all_html = True`
`501`	`502`	`# serve_xss_vulnerable_mimetypes = False`
`502`	`503`	`# track_jobs_in_database = None`
`503`		`- # outputs_to_working_directory = False`
`504`	`504`	`# retry_job_output_collection = 0`
`505`	`505`
`506`	`506`	`env = _build_env_for_galaxy(properties, template_args)`