All,
I manage a cluster and have been asked to set up a local instance of galaxy. I'm neither a galaxy user nor a biologist, so apologies in advance if my terminology is off.
I have a basic setup running now, but have been asked to include the option to "display at UCSC Main" when a user uploads a bam and clicks on the dataset. Currently I have the options of "display in IGB Local Web". I've tried this at a few of the other Galaxy sites, and the behavior seems unpredictable. Uploading the same data set to some sites gives me this option, while others don't. I'm assuming this is determined by the option in the universe_wsgi.ini file:
# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt ucsc_display_sites = main,test,archaea,ucla
but uncommenting this option and restarting the server doesn't help. Increasing the log_level to DEBUG doesn't provide any insight.
Any suggestions about how to proceed? Could there be any firewall-related issues? I ask because of this in the configuration file:
# If use_remote_user = True, display application servers will be denied access # to Galaxy and so displaying datasets in these sites will fail. # display_servers contains a list of hostnames which should be allowed to # bypass security to display datasets. Please be aware that there are security # implications if this is allowed. More details (including required changes to # the proxy server config) are available in the Apache proxy documentation on # the wiki.
Thanks in advance, Malcolm