release 1.0.1

• copy nginx conf from file or template
• define required param in config_example.yml
• fix species folder name (remove -)
• fix mount of unused galaxy_data_libs.py in docker-compose file

gga_init.py

@@ -79,11 +79,10 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         # Create nginx dirs and write/re-write nginx conf
         make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
         try:
-            with open(os.path.abspath("./nginx/conf/default.conf"), 'w') as conf:
-                conf.write("server {\n\tlisten 80;\n\tserver_name ~.;\n\tlocation /download/ {\n\t\talias /project_data/; \n\t\tautoindex on;\n\t}\n}")  # The species nginx conf
-        except OSError as exc:
-            logging.critical("Cannot edit NginX conf file")
-            sys.exit(exc)
+            shutil.copy(os.path.join(self.script_dir, "files/nginx_download.conf"), os.path.abspath("./nginx/conf/default.conf"))
+        except Exception as exc:
+            logging.critical("Could not copy nginx configuration file for %s" % self.full_name)
+            logging.critical(exc)            
 
         # Return to main directory
         os.chdir(self.main_dir)
@@ -107,7 +106,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
 
         # Jinja2 templating, handled using the python "jinja2" module
         file_loader = FileSystemLoader(self.script_dir + "/templates")
-        env = Environment(loader=file_loader)
+        env = Environment(loader=file_loader, trim_blocks=True, lstrip_blocks=True)
 
         # We need a dict holding all key (variables) - values that needs to be replaced in the template as our rendering dict
         # To do so we need both input file vars and config vars
@@ -127,6 +126,14 @@ class DeploySpeciesStack(speciesData.SpeciesData):
             gspecies_compose_file.truncate(0)
             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)
+
         # Create the volumes (directory) of the species docker-compose file
         create_mounts(working_dir=".", main_dir=self.main_dir)
 
@@ -202,7 +209,7 @@ def make_traefik_compose_files(config, main_dir):
                 traefik_compose_file.truncate(0)
                 traefik_compose_file.write(traefik_compose_output)
 
-        if config["authelia_config_path"]:
+        if "authelia_config_path" in config.keys():
             if not config["authelia_config_path"] == "" or not config["authelia_config_path"] == "/path/to/authelia/config":
                 if os.path.isfile(os.path.abspath(config["authelia_config_path"])):
                     try:
@@ -217,11 +224,14 @@ def make_traefik_compose_files(config, main_dir):
                     #     authelia_config_file.truncate(0)
                     #     authelia_config_file.write(authelia_config_output)
                 else:
-                    logging.critical("Cannot find authelia configuration template path (%s)" % config["authelia_config_path"])
+                    logging.critical("Cannot find authelia configuration path (%s)" % config["authelia_config_path"])
                     sys.exit()
+            else:
+                logging.critical("Invalid authelia configuration path (%s)" % config["authelia_config_path"])
+                sys.exit()
 
         # Path to the authelia users in the repo
-        authelia_users_path = script_dir + "/templates/authelia_users_template.yml"
+        authelia_users_path = script_dir + "/files/authelia_users_template.yml"
         # Copy authelia "users" file
         if not os.path.isfile("./traefik/authelia/users.yml"):
             shutil.copy(authelia_users_path, "./traefik/authelia/users.yml")