Hi,
I am not sure if I understand correctly how the external data sources (i.e. BioMart) are integrated into Galaxy. However, I believe that the Galaxy sends an HTTP request to the external data source with the parameter GALAXY_URL - and this URL is used later by the external data source to send parameters for a subsequent request resubmission. Without going to further details (about sync and async method), it seems to me that in any case the URL given in GALAXY_URL must be a publicly available URL (available from/by the external source).
1) But what if I am running my own Galaxy behind a firewall that does not allow access from the outside?
2) If I cannot make our firewall open, is there a way (perhaps in the Galaxy configuration) to change the host name that Galaxy is using when creating its GALAXY_URL parameter? That would allow me have a "third-party" URL where Galaxy and external data sources can communicate together.
Many thanks for any help, Martin