Hi again, I've done with plugging our local UCSC mirror into galaxy. I'm able to view most of the data except for BAM and bigWig files. I'm adding bigWig as new datatype as we mostly work with that. Besides the fact I'm not able to sniff properly the bigWig data type (but I still can define the type at import time), I'm not able to view in UCSC. Essentially I've copied the ucsc/bam.xml file and edited to enable bigWig tracks. The problem now is that BAM (or bigWig) can't be viewed by the UCSC because of authentication issues :-( The UCSC mirrors says that this address
http://host001.instruments.ifom-ieo-campus.it:8080/display_application/917af...
generated by galaxy cannot be viewed (auth required)... Indeed this URL format differs from the one defined for bed files which is in the form of HOST:PORT/root/display_as?PARAMS. The latter has a special configuration in my apache conf file (as suggested by Nate and others), but the same conf for
<Location /display_application>
doesn't work (I believe this depends on /lib/galaxy/web/framework/middleware/remoteuser.py implementation).
d /* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */