Hi,

I tried your advice but my problem is persistent.
In "tool-data/shared/ucsc/ucsc_build_sites.txt", I added :
"#Harvested from http://ucsc.igf.cnrs.fr/cgi-bin/das/dsn
mgx     http://ucsc.igf.cnrs.fr/cgi-bin/hgTracks?       hg19,mm9,dm3,droSim1,droYak2,dp3,droVir2,sacCer2,Emihu1,Xnematophila,ZmB73_AGPv1,Athaliana_tair9,sma_v3_1"

But when I try http://ucsc.igf.cnrs.fr/cgi-bin/das/dsn on my web browser, I haven't the good server :

<DASDSN>
−
<DSN>
<SOURCE id="hg19" version="1.00">GRCh37 at UCSC</SOURCE>
<DESCRIPTION>Human GRCh37 Genome at UCSC</DESCRIPTION>
<MAPMASTER>MailScanner soupçonne le lien suivant d'être une tentative de fraude de la part de "genome.cse.ucsc.educgi-bin" http://genome.cse.ucsc.edu:80/cgi-bin/das/hg19</MAPMASTER>
</DSN>
−
<DSN>
<SOURCE id="mm9" version="1.00">July 2007 at UCSC</SOURCE>
<DESCRIPTION>Mouse July 2007 Genome at UCSC</DESCRIPTION>
<MAPMASTER>MailScanner soupçonne le lien suivant d'être une tentative de fraude de la part de "genome.cse.ucsc.educgi-bin" http://genome.cse.ucsc.edu:80/cgi-bin/das/mm9</MAPMASTER>
</DSN>
−
<DSN>
<SOURCE id="Emihu1" version="1.00">April 25, 2008 at UCSC</SOURCE>
<DESCRIPTION>E. huxleyi April 25, 2008 Genome at UCSC</DESCRIPTION>
<MAPMASTER>MailScanner soupçonne le lien suivant d'être une tentative de fraude de la part de "genome.cse.ucsc.educgi-bin" http://genome.cse.ucsc.edu:80/cgi-bin/das/Emihu1</MAPMASTER>
</DSN>
−
<DSN>
<SOURCE id="Xnematophila" version="1.00">date inconnue at UCSC</SOURCE>
<DESCRIPTION>X. nematophila date inconnue Genome at UCSC</DESCRIPTION>
−
<MAPMASTER>
MailScanner soupçonne le lien suivant d'être une tentative de fraude de la part de "genome.cse.ucsc.educgi-bin" http://genome.cse.ucsc.edu:80/cgi-bin/das/Xnematophila
</MAPMASTER>
</DSN>
−
<DSN>
<SOURCE id="ZmB73_AGPv1" version="1.00">2009-03-20 at UCSC</SOURCE>
<DESCRIPTION>Z. mays B73 2009-03-20 Genome at UCSC</DESCRIPTION>
−
<MAPMASTER>
MailScanner soupçonne le lien suivant d'être une tentative de fraude de la part de "genome.cse.ucsc.educgi-bin" http://genome.cse.ucsc.edu:80/cgi-bin/das/ZmB73_AGPv1
</MAPMASTER>
</DSN>
−
<DSN>

Have you an idea how change this ?

Thanks,

Emeric

 
*****************************************

Emeric Dubois
Plateforme MGX
Institut de Génomique Fonctionnelle
UMR 5203 CNRS – U 661 INSERM – Universite de Montpellier
141 rue de la cardonille
34094 Montpellier Cedex 05, France
Tel: 04 67 14 29 32

Emeric.Dubois@igf.cnrs.fr

*****************************************

Le 14/04/2010 23:05, Lee, Joshua a écrit :

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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