Hi Nate, hi galaxy devlps On May 25, 2010, at 9:23 PM, Nate Coraor wrote:
Davide Cittaro wrote:
Still I have to fix the display on external ucsc mirrors, according to your wiki page I should set: <Location /root/display_as> Satisfy Any Order deny,allow Deny from all Allow from genome.ifom-ieo-campus.it <http://genome.ifom-ieo-campus.it> Allow from host036.2b11.ifom-ieo-campus.it <http://host036.2b11.ifom-ieo-campus.it> </Location> The first is our local mirror, the second is a test workstation... I'm getting 401 errors... Mmmm....
Hi Davide,
I just tested this config in Apache and it still works for me. Anything helpful in the Apache error log?
I found what was wrong, essentially this galaxy instance is not public to the world, hence I cannot use UCSC sites from cse.edu. I have to link to our local mirror (which is behind our main proxy too). I thought I only had to enable it in the universe_wsgi.ini file: ucsc_display_sites = main,campus and $ grep campus tool-data/shared/ucsc/ucsc_build_sites.txt #Harvested from http://genome.ifom-ieo-campus.it/cgi-bin/das/dsn campus http://genome.ifom-ieo-campus.it/cgi-bin/hgTracks? hg19,hg18,hg17,mm9,mm8,rn4,danRer6,danRer5,ci2,ce6,ce4,cb3,dm3,sacCer2,sacCer1 Unfortunately this is not enough, as UCSC sites are hardcoded in galaxy. Some greps and debugs led me to this diff: $ diff -u remoteuser.here.py remoteuser.py --- remoteuser.here.py 2010-05-26 12:19:30.349424733 +0200 +++ remoteuser.py 2010-05-26 12:19:51.968985808 +0200 @@ -44,7 +44,6 @@ 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu', - 'genome.ifom-ieo-campus.it', ) UCSC_ARCHAEA_SERVERS = ( 'lowepub.cse.ucsc.edu', @@ -56,7 +55,7 @@ self.maildomain = maildomain self.allow_ucsc_main = False self.allow_ucsc_archaea = False - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'campus' in ucsc_display_sites: + if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: self.allow_ucsc_archaea = True Now I can link our local mirror (at least for intervals, still have to try with BAM files). I'm only afraid that I will lose these changes in the next repository upgrade... Should I open a bug request to remove hardcoded links or you are already working on this? cheers 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 */