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=...

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 -- Ce message a été vérifié par MailScanner pour des virus ou des polluriels et rien de suspect n'a été trouvé. _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

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">

<DASDSN>

<DSN>

<SOURCE id="hg18" version="1.00">Mar. 2006 at UCSC</SOURCE>

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

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

</DSN>

<DSN>

<SOURCE id="mm9" version="1.00">July 2007 at UCSC</SOURCE>

<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 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 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 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 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 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=...

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 -- Ce message a été vérifié par MailScanner pour des virus ou des polluriels et rien de suspect n'a été trouvé. _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev