Hi,
I don’t know if you have figured out a solution to this,
but I encountered a similar problem and found a workaround.
It seems that you have reconfigured UCSC main to instead point
to your local instance. In my case, I added a new “local” instance of
the browser to Galaxy by adding a line to tool-data/shared/ucsc/ucsc_build_sites.txt
rather than modifying “main”.
My workaround is to add the host to the list UCSC_SERVERS in lib/galaxy/web/framework/__init__.py.
This will prevent __ensure_logged_in_user from doing a send_redirect to “/root/index”.
Also of note, in lib/galaxy/security/__init__.py, you may need to modify the “sites”
variable so the hosts are correct.
Ideally, this would be configurable outside the source code, but
this method is working for me so far.
Josh
From: galaxy-dev-bounces@lists.bx.psu.edu
[mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Emeric Dubois
Sent: Tuesday, April 13, 2010 4:19 AM
To: Daniel Blankenberg
Cc: galaxy-dev@bx.psu.edu
Subject: Re: [galaxy-dev] display at UCSC
Hello
UCSC local miror (user on server is "ucsc") and galaxy (user on
server is "galaxy") are on the same server.
Galaxy is configured with prefix (http://aura.igf.cnrs.fr/galaxy/)
and access is only on your network.
Many parameters :
require_login = True
allow_user_creation = False
new_user_dataset_access_role_default_private = True
Apache configuration :
NameVirtualHost *:80
<VirtualHost *:80>
ServerAdmin mgx@igf.cnrs.fr
DocumentRoot /var/www/html/
ServerName aura.igf.cnrs.fr/galaxy
ServerAlias galaxy
RewriteEngine On
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) /usr/local/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/(.*) /usr/local/galaxy/static/$1 [L]
RewriteRule ^/static/(.*) /usr/local/galaxy/static/$1 [L]
RewriteRule ^/galaxy/static/MGX/(.*) /usr/local/galaxy/static/MGX/$1 [L]
RewriteRule ^/galaxy/images/(.*) /usr/local/galaxy/static/images/$1 [L]
RewriteRule ^/galaxy/favicon.ico /usr/local/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /usr/local/galaxy/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
<Location /galaxy/root/display_as>
Satisfy Any
Order deny,allow
Deny from all
Allow from hgw1.cse.ucsc.edu
Allow from hgw2.cse.ucsc.edu
Allow from hgw3.cse.ucsc.edu
Allow from hgw4.cse.ucsc.edu
Allow from hgw5.cse.ucsc.edu
Allow from hgw6.cse.ucsc.edu
Allow from hgw7.cse.ucsc.edu
Allow from hgw8.cse.ucsc.edu
Allow from ucsc.igf.cnrs.fr
Allow from ucsc
Allow from genome-test.cse.ucsc.edu
Allow from aura.igf.cnrs.fr
</Location>
</VirtualHost>
The link target is :
http://aura.igf.cnrs.fr/galaxy/datasets/4/display_at/ucsc_main?redirect_url=http%3A%2F%2Fucsc.igf.cnrs.fr%2Fcgi-bin%2FhgTracks%3Fdb%3Dhg18%26position%3Dchr1%3A8406334-100590610%26hgt.customText%3D%25s&display_url=http%3A%2F%2Faura.igf.cnrs.fr%2Fgalaxy%2Froot%2Fdisplay_as%3Fid%3D4%26display_app%3Ducsc%26authz_method%3Ddisplay_at
tool-data/shared/ucsc/ucsc_build_sites.txt file :
#Harvested from http://ucsc.igf.cnrs.fr/cgi-bin/das/dsn
# MODIF MGX
main http://ucsc.igf.cnrs.fr/cgi-bin/hgTracks?
priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2,Emihu1,Xnematophila,ZmB73_AGPv1,Athaliana_tair9,sma_v3_1
## FIN MODIF MGX
Thanks for your help
Emeric
Le 12/04/2010 17:34, Daniel Blankenberg a écrit :
Hi Emeric,
Can you provide some more information about your server configuration? Are you running Galaxy away from the server root? What is the link that is generated by Galaxy (right click, copy the link target, and paste back to us)? Also, what are the contents of the tool-data/shared/ucsc/ucsc_build_sites.txt file?
Thanks,
Dan
On Apr 7, 2010, at 9:12 AM, Emeric Dubois wrote:
Hello
I have installed Galaxy in a production environment and a UCSC local mirror.
When I click on "display at UCSC main", I have an error on UCSC :
"redirected to non-http(s): /galaxy/root"
Have you an idea to resolve this problem ?
Thanks
Emeric
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