Corrections cloud

run_workflow_phaeoexplorer.py

@@ -492,9 +492,12 @@ class RunWorkflow(speciesData.SpeciesData):
             # In case of the Jbrowse workflow, we unfortunately have to manually edit the parameters instead of setting them
             # as runtime values, using runtime parameters makes the tool throw an internal critical error ("replace not found" error)
             # Scratchgmod test: need "http" (or "https"), the hostname (+ port)
-            # TODO --> use menu_url variable in config to set up the menu url
+            if "menu_url" not in self.config.keys():
+                jbrowse_menu_url = "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")
+            else:
+                jbrowse_menu_url = self.config["menu_url"]
             if workflow_name == "Jbrowse":
-                workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}"))
+                workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", jbrowse_menu_url)
                 # The UNIQUE_ID is specific to a combination genus_species_strain_sex so every combination should have its unique workflow
                 # in galaxy --> define a naming method for these workflows
                 workflow_dict["steps"]["3"]["tool_state"] = workflow_dict["steps"]["3"]["tool_state"].replace("__FULL_NAME__", self.full_name).replace("__UNIQUE_ID__", self.species_folder_name)