I am trying to configure Galaxy v18.09 wtih sub-uri. In prior 18.01, I use this configuration in conjunction with Apache rewrite rules and it works well: [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /msgalaxy [app:main] filter-with = proxy-prefix cookie_path = '/galaxy' In galaxy.yml, I know I need to uncomment and add the following filter-with: proxy-prefix cookie_path: '/galaxy' However, I don't know where and how to add filter:proxy-prefix. The comment in config.yml says: # If running behind a proxy server and Galaxy is served from a # subdirectory, enable the proxy-prefix filter and set the prefix in # the [filter:proxy-prefix] section above. which is for galaxy.ini file. An example on how to do it would be much appreciated. Ping