Workflow v2

gga_init.py

@@ -127,12 +127,13 @@ class DeploySpeciesStack(speciesData.SpeciesData):
             gspecies_compose_file.write(gspecies_compose_output)
 
 
-        galaxy_nginx_conf_template = env.get_template("galaxy_nginx.conf.j2")
-        galaxy_nginx_conf_output = galaxy_nginx_conf_template.render(render_vars)
-        with open(os.path.join(self.main_dir, "galaxy_nginx.conf"), "w") as galaxy_nginx_conf_file:
-            logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)
-            galaxy_nginx_conf_file.truncate(0)
-            galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
+        if not os.path.isfile(os.path.join(self.main_dir, "galaxy_nginx.conf")):
+            galaxy_nginx_conf_template = env.get_template("galaxy_nginx.conf.j2")
+            galaxy_nginx_conf_output = galaxy_nginx_conf_template.render(render_vars)
+            with open(os.path.join(self.main_dir, "galaxy_nginx.conf"), "w") as galaxy_nginx_conf_file:
+                logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)
+                galaxy_nginx_conf_file.truncate(0)
+                galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
 
         # Create the volumes (directory) of the species docker-compose file
         create_mounts(working_dir=".", main_dir=self.main_dir)