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

@@ -76,13 +76,37 @@ class DeploySpeciesStack(speciesData.SpeciesData):
             logging.debug("Using default banner for Tripal pages")
             self.config.pop("banner_path", None)
 
+
+        # Write galaxy_nginx.conf
+        try:
+            with open(os.path.abspath(os.path.join(self.script_dir, "galaxy_nginx.conf")), "w") as galaxy_nginx_conf:
+                galaxy_nginx_conf.truncate(0)
+                galaxy_nginx_conf.write("uwsgi_param  QUERY_STRING       $query_string;")
+                galaxy_nginx_conf.write("uwsgi_param  REQUEST_METHOD     $request_method;")
+                galaxy_nginx_conf.write("uwsgi_param  CONTENT_TYPE       $content_type;")
+                galaxy_nginx_conf.write("uwsgi_param  CONTENT_LENGTH     $content_length;")
+                galaxy_nginx_conf.write("uwsgi_param  REQUEST_URI        $request_uri;")
+                galaxy_nginx_conf.write("uwsgi_param  PATH_INFO          $document_uri;")
+                galaxy_nginx_conf.write("uwsgi_param  DOCUMENT_ROOT      $document_root;")
+                galaxy_nginx_conf.write("uwsgi_param  SERVER_PROTOCOL    $server_protocol;")
+                galaxy_nginx_conf.write("uwsgi_param  REQUEST_SCHEME     $scheme;")
+                galaxy_nginx_conf.write("uwsgi_param  HTTPS              $https if_not_empty;")
+                galaxy_nginx_conf.write("uwsgi_param  REMOTE_ADDR        $remote_addr;")
+                galaxy_nginx_conf.write("uwsgi_param  REMOTE_PORT        $remote_port;")
+                galaxy_nginx_conf.write("uwsgi_param  SERVER_PORT        $server_port;")
+                galaxy_nginx_conf.write("uwsgi_param  SERVER_NAME        $server_name;")
+                galaxy_nginx_conf.write("uwsgi_param HTTP_REMOTE_USER gga;")
+        except OSError as exc:
+            logging.critical("Cannot write galaxy NginX conf file (%s)" % os.path.abspath(self.script_dir))
+            sys.exit(exc)
+
         # 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")
+            logging.critical("Cannot write NginX conf file")
             sys.exit(exc)
 
         # Return to main directory