James Casbon wrote:
When attempting to display a custom track on the UCSC genome browser, galaxy generates a URL such as...
The first problem I have is that the base url is wrong for the customText - I am using https - is there a way to set that?
This is a function of the Apache proxy. You connect to Apache via https, but it proxies to Galaxy via http. I wrote a fix for this but haven't committed it; I just learned that the browser doesn't support https. You could do some Apache trickery to make this work (i.e. use Location directives in your http VirtualHost to only allow through UCSC on http connections).
The customText parameter is the bit that allows UCSC to pick up the data - but it is not going to get past the external auth. Is there a reasonable way to fix this? I suppose there must be a way to bypass the auth if the request comes from UCSC and looks like a certain URL, but is there a better way?
The solution for this is provided here, but please be aware that it opens up a security hole: http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy#DisplayatUCSC I have a couple ideas about how to close this hole but nothing planned as of yet. --nate