diff --git a/gga_load_data.py b/gga_load_data.py index 9d2277017b38b2ab97253892967248945a584cd5..655f78aa3f18bef68b6cc9fafd1920a159ae9388 100755 --- a/gga_load_data.py +++ b/gga_load_data.py @@ -101,7 +101,7 @@ class LoadData(speciesData.SpeciesData): return histories - def setup_library(self, instance, data_dir_root='./src_data'): + def setup_library(self, data_dir_root='./src_data'): """ Create a "Project Data" library in galaxy, mirroring the "src_data" folder of the current organism directory tree @@ -111,7 +111,7 @@ class LoadData(speciesData.SpeciesData): self.goto_species_dir() - gio = GalaxyInstance(url=self.instance_url, + instance = GalaxyInstance(url=self.instance_url, email=self.config["galaxy_default_admin_email"], password=self.config["galaxy_default_admin_password"] ) @@ -372,7 +372,7 @@ if __name__ == "__main__": # Load the datasets into a galaxy library logging.info("Setting up library for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species)) - load_data_for_current_species.setup_library(load_data_for_current_species.instance) + load_data_for_current_species.setup_library() logging.debug("Successfully set up library in galaxy for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species)) # Set or get the history for the current organism