diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py index 89a0718d1cc94c07723729871b9db749e9ecbb79..96f141ef90a5aedc272b057dd351e6ca62b8b9b9 100644 --- a/gga_run_workflow_phaeo_jbrowse.py +++ b/gga_run_workflow_phaeo_jbrowse.py @@ -82,7 +82,7 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow): self.transcripts_hda_id = None self.proteins_hda_id = None - def install_changesets_revisions_for_individual_tools(self): + def install_individual_tools(self): """ This function is used to verify that installed tools called outside workflows have the correct versions and changesets If it finds versions don't match, will install the correct version + changeset in the instance @@ -273,7 +273,7 @@ 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_changesets_revisions_for_individual_tools() + run_workflow_for_current_organism.install_individual_tools() run_workflow_for_current_organism.import_datasets_into_history() analyses_dict_list = run_workflow_for_current_organism.get_analyses() @@ -391,7 +391,7 @@ if __name__ == "__main__": workflow_path = os.path.join(os.path.abspath(script_dir), constants_phaeo.WORKFLOWS_PATH, constants_phaeo.WF_LOAD_GFF_JB_1_ORG_FILE) # Check if the versions of tools specified in the workflow are installed in galaxy - utilities_bioblend.install_changesets_revisions_from_workflow(workflow_path=workflow_path, instance=org_wf_param.instance) + utilities_bioblend.install_workflow_tools(workflow_path=workflow_path, instance=org_wf_param.instance) # Set the workflow parameters (individual tools runtime parameters in the workflow) workflow_parameters = {} @@ -484,7 +484,7 @@ if __name__ == "__main__": workflow_path = os.path.join(os.path.abspath(script_dir), constants_phaeo.WORKFLOWS_PATH, constants_phaeo.WF_LOAD_GFF_JB_2_ORG_FILE) # Check if the versions of tools specified in the workflow are installed in galaxy - utilities_bioblend.install_changesets_revisions_from_workflow(workflow_path=workflow_path, instance=sp_wf_param_org1.instance) + utilities_bioblend.install_workflow_tools(workflow_path=workflow_path, instance=sp_wf_param_org1.instance) # Set the workflow parameters (individual tools runtime parameters in the workflow) workflow_parameters = {} diff --git a/utilities_bioblend.py b/utilities_bioblend.py index dc19d0e5b5643bc143b5c869da519d4ea509e299..3cfcc4857e6ae58ac51553e51c3e8438788adf60 100644 --- a/utilities_bioblend.py +++ b/utilities_bioblend.py @@ -139,7 +139,7 @@ def install_repository_revision(instance, tool_id, version, changeset_revision): install_repository_dependencies=False, install_resolver_dependencies=True) -def install_changesets_revisions_from_workflow(instance, workflow_path): +def install_workflow_tools(instance, workflow_path): """ Read a .ga file to extract the information about the different tools called. Check if every tool is installed via a "show_tool".