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

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