diff --git a/gga_init.py b/gga_init.py index d5fc63f0a3e4b754c330ff60e87dd44b7539a4ad..e630db1238f396cdd0e294c8d38d02058bb77561 100755 --- a/gga_init.py +++ b/gga_init.py @@ -126,19 +126,11 @@ class DeploySpeciesStack(speciesData.SpeciesData): # To do so we need both input file vars and config vars # Create input file vars dict - input_vars = {} - if self.picture_path is not None: - input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species, + input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species, "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name, "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species.lower(), self.sex), "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:], "blast": self.blast, "picture_path": self.picture_path} - else: - input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species, - "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name, - "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species.lower(), self.sex), - "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:], - "blast": self.blast} if (len(self.config.keys()) == 0): logging.error("Empty config dictionary") # Merge the two dicts diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2 index 22e8c29d7e9f607f73bdd55e6c1a85517afc0d21..9a05ccfc4c8abfee341532cf0e2464714a8882cc 100644 --- a/templates/organisms.yml.j2 +++ b/templates/organisms.yml.j2 @@ -6,9 +6,7 @@ {{ org_param_desc_strain }}: {{ org_param_desc_strain_value }} {{ org_param_desc_common_name }}: {{ org_param_desc_common_name_value }} {{ org_param_desc_origin }}: {{ org_param_desc_origin_value }} - {% if org_param_desc_picture_path_value is defined %} {{ org_param_desc_picture_path }}: {{ org_param_desc_picture_path_value }} - {% endif %} {% if org_param_desc_main_species_value is defined and org_param_desc_main_species_value is sameas true %} {{ org_param_desc_main_species }}: yes {% endif %}