diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py index 70f6387e49591e7ea61949e632d814f43b0eeb43..67968163a8b287877e09e298a0c67b771a8c9288 100644 --- a/run_workflow_phaeoexplorer.py +++ b/run_workflow_phaeoexplorer.py @@ -235,7 +235,7 @@ 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) if workflow_name == "Jbrowse": - workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", "http://{hostname}:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], port=self.config["http_port"], 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__", "http://localhost:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(port=self.config["http_port"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")) workflow_dict["steps"]["3"]["tool_state"] = workflow_dict["steps"]["3"]["tool_state"].replace("__FULL_NAME__", self.full_name).replace("__UNIQUE_ID__", self.abbreviation) # Import the workflow in galaxy as a dict @@ -594,15 +594,9 @@ if __name__ == "__main__": # Parse the config yaml file run_workflow_for_current_organism.config = utilities.parse_config(args.config) # Set the instance url attribute - for env_variable, value in run_workflow_for_current_organism.config.items(): - if env_variable == "hostname": - run_workflow_for_current_organism.instance_url = "http://{0}:8888/sp/{1}/galaxy/".format( - value, run_workflow_for_current_organism.genus_species) - break - else: - run_workflow_for_current_organism.instance_url = "http://localhost:8888/sp/{0}_{1}/galaxy/".format( - run_workflow_for_current_organism.genus_lowercase, - run_workflow_for_current_organism.species) + run_workflow_for_current_organism.instance_url = "http://localhost:8888/sp/{0}_{1}/galaxy/".format( + run_workflow_for_current_organism.genus_lowercase, + run_workflow_for_current_organism.species) # If input workflow is Chado_load_Tripal_synchronize.ga if "Chado_load_Tripal_synchronize" in str(workflow):