diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py index b7a9a24e91385c3bda8532ff7045e166d0a366ba..f73976f51cbf94e082e9d1163e86a9c077b9d406 100644 --- a/gga_run_workflow_phaeo_jbrowse.py +++ b/gga_run_workflow_phaeo_jbrowse.py @@ -171,7 +171,7 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow): return org_id - def import_datasets_into_history(self): + def import_datasets_into_history(self, config): """ Find datasets in a library, get their ID and import them into the current history if they are not already """ @@ -187,8 +187,8 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow): proteins_hda_id = None gio = GalaxyInstance(url=self.instance_url, - email=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_EMAIL], - password=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_PASSWORD] + email=config[constants.CONF_GALAXY_DEFAULT_ADMIN_EMAIL], + password=config[constants.CONF_GALAXY_DEFAULT_ADMIN_PASSWORD] ) prj_lib = gio.libraries.get_previews(constants.GALAXY_LIBRARY_NAME) if len(prj_lib) == 1: @@ -284,7 +284,7 @@ def prepare_history_and_get_wf_param(sp_dict_list, main_dir, config): run_workflow_for_current_organism.set_galaxy_instance(config) run_workflow_for_current_organism.set_history() run_workflow_for_current_organism.install_individual_tools() - run_workflow_for_current_organism.import_datasets_into_history() + run_workflow_for_current_organism.import_datasets_into_history(config) analyses_dict_list = run_workflow_for_current_organism.get_analyses()