Hi Emeric,

Here is the line I added my ucsc_build_sites.txt:

local http://my.ip/GenomeBrowser/cgi-bin/hgTracks? hg18

When I hit http://my.ip/GenomeBrowser/cgi-bin/das/dsn, I get:

<?xml version="1.0" standalone="no"?>

<!DOCTYPE DASDSN SYSTEM "http://www.biodas.org/dtd/dasdsn.dtd">

<DSN>

<DESCRIPTION>Human Mar. 2006 Genome at UCSC</DESCRIPTION>

<MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg18</MAPMASTER>

</DSN>

<DSN>

<DESCRIPTION>Mouse July 2007 Genome at UCSC</DESCRIPTION>

<MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/mm9</MAPMASTER>

</DSN>

</DASDSN>

I’m not really familiar with the significance of this script, so I can’t speak much to the error you are getting. I don’t believe I made any tweaks besides those two __init__.py files and ucsc_build_sites.txt. I am not using Apache and am actually currently serving Genome Browser through Tomcat.

Josh

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Emeric Dubois
Sent: Thursday, April 15, 2010 4:39 AM
To: Lee, Joshua
Cc: galaxy-dev@bx.psu.edu
Subject: [galaxy-dev] {Disarmed} Re: display at UCSC

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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