Hi, I've been using the subversion version of Galaxy for a while, but now I want to update to the latest mercurial release. I installed it in a new location as per the wiki and set-up the SGE settings as per my previous install and all the tests pass. It launches fine, but when viewing the website the frames seem to be off-by-one. i.e., the 'Tools' frame is empty except for "This link may not be followed from within Galaxy.", the tools are in the middle window and the 'History' frame has general information. I can't see any errors in the paster.log file, so where can I look to sort out this error? Thanks, Chris
Hi Chris, It sounds like you maybe be running through a proxy, away from the server root, without the proxy-prefix option set in universe_wsgi.ini? If so, have a look at the documentation here: http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy#Apacheconfigurationw... --nate Chris Cole wrote:
Hi,
I've been using the subversion version of Galaxy for a while, but now I want to update to the latest mercurial release.
I installed it in a new location as per the wiki and set-up the SGE settings as per my previous install and all the tests pass. It launches fine, but when viewing the website the frames seem to be off-by-one. i.e., the 'Tools' frame is empty except for "This link may not be followed from within Galaxy.", the tools are in the middle window and the 'History' frame has general information.
I can't see any errors in the paster.log file, so where can I look to sort out this error? Thanks,
Chris _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Nate, in the URL you just sent, are the "Apache configuration with Galaxy not at the web server root" and "External authentication and $REMOTE_USER" mutually exclusive? cheers, Erick 2009/7/3 Nate Coraor <nate@bx.psu.edu>
Hi Chris,
It sounds like you maybe be running through a proxy, away from the server root, without the proxy-prefix option set in universe_wsgi.ini? If so, have a look at the documentation here:
http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy#Apacheconfigurationw...
--nate
Chris Cole wrote:
Hi,
I've been using the subversion version of Galaxy for a while, but now I want to update to the latest mercurial release.
I installed it in a new location as per the wiki and set-up the SGE settings as per my previous install and all the tests pass. It launches fine, but when viewing the website the frames seem to be off-by-one. i.e., the 'Tools' frame is empty except for "This link may not be followed from within Galaxy.", the tools are in the middle window and the 'History' frame has general information.
I can't see any errors in the paster.log file, so where can I look to sort out this error? Thanks,
Chris _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Erick Antezana wrote:
Nate,
in the URL you just sent, are the "Apache configuration with Galaxy not at the web server root" and "External authentication and $REMOTE_USER" mutually exclusive?
cheers, Erick
Not at all. Here's a sample configuration: <Location /galaxy> AuthType Basic AuthName Galaxy AuthUserFile /htpasswd Require valid-user </Location> # Required to pass REMOTE_USER <Proxy http://127.0.0.1:8080> Order deny,allow Allow from all </Proxy> RewriteEngine on RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P] --nate
Nate, thanks for the piece of code. It worked perfectly on my test server. However, when I tried to put it the production serve, whose apache makes use of VirtualServers in contrast to my test server, it didn't work :-( I am able to authenticate using my ldap login/password but then the web site shows just a blank page... there is no message in paster.log; however, the apache log says: [Tue Jul 07 09:35:29 2009] [error] PHP Warning: include(/apache/prod/html/php/menuLoader.php) [<a href='function.include'>function.include</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Warning: include() [<a href='function.include'>function.include</a>]: Failed opening '/apache/prod/html/php/menuLoader.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/galaxy [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/favicon.ico, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/ Do you know what could be the problem? thanks, Erick 2009/7/3 Nate Coraor <nate@bx.psu.edu>
Erick Antezana wrote:
Nate,
in the URL you just sent, are the "Apache configuration with Galaxy not at the web server root" and "External authentication and $REMOTE_USER" mutually exclusive?
cheers, Erick
Not at all. Here's a sample configuration:
<Location /galaxy> AuthType Basic AuthName Galaxy AuthUserFile /htpasswd Require valid-user </Location>
# Required to pass REMOTE_USER <Proxy http://127.0.0.1:8080> Order deny,allow Allow from all </Proxy>
RewriteEngine on
RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P]
--nate
Any idea what's generating all the PHP errors? This is unrelated to Galaxy. Erick Antezana wrote:
Nate,
thanks for the piece of code. It worked perfectly on my test server. However, when I tried to put it the production serve, whose apache makes use of VirtualServers in contrast to my test server, it didn't work :-( I am able to authenticate using my ldap login/password but then the web site shows just a blank page... there is no message in paster.log; however, the apache log says:
[Tue Jul 07 09:35:29 2009] [error] PHP Warning: include(/apache/prod/html/php/menuLoader.php) [<a href='function.include'>function.include</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Warning: include() [<a href='function.include'>function.include</a>]: Failed opening '/apache/prod/html/php/menuLoader.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/galaxy [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/favicon.ico, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/
Do you know what could be the problem?
thanks, Erick
2009/7/3 Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu>>
Erick Antezana wrote:
Nate,
in the URL you just sent, are the "Apache configuration with Galaxy not at the web server root" and "External authentication and $REMOTE_USER" mutually exclusive?
cheers, Erick
Not at all. Here's a sample configuration:
<Location /galaxy> AuthType Basic AuthName Galaxy AuthUserFile /htpasswd Require valid-user </Location>
# Required to pass REMOTE_USER <Proxy http://127.0.0.1:8080> Order deny,allow Allow from all </Proxy>
RewriteEngine on
RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P]
--nate
Hi Nate, yes, those PHP lines were just noise from the file... Anyway, we fixed the problem by removing the Virtual servers. SO everything is working fine. thanks Erick 2009/7/13 Nate Coraor <nate@bx.psu.edu>
Any idea what's generating all the PHP errors? This is unrelated to Galaxy.
Erick Antezana wrote:
Nate,
thanks for the piece of code. It worked perfectly on my test server. However, when I tried to put it the production serve, whose apache makes use of VirtualServers in contrast to my test server, it didn't work :-( I am able to authenticate using my ldap login/password but then the web site shows just a blank page... there is no message in paster.log; however, the apache log says:
[Tue Jul 07 09:35:29 2009] [error] PHP Warning: include(/apache/prod/html/php/menuLoader.php) [<a href='function.include'>function.include</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Warning: include() [<a href='function.include'>function.include</a>]: Failed opening '/apache/prod/html/php/menuLoader.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/galaxy [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/favicon.ico, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/
Do you know what could be the problem?
thanks, Erick
2009/7/3 Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu>>
Erick Antezana wrote:
Nate,
in the URL you just sent, are the "Apache configuration with Galaxy not at the web server root" and "External authentication and $REMOTE_USER" mutually exclusive?
cheers, Erick
Not at all. Here's a sample configuration:
<Location /galaxy> AuthType Basic AuthName Galaxy AuthUserFile /htpasswd Require valid-user </Location>
# Required to pass REMOTE_USER <Proxy http://127.0.0.1:8080> Order deny,allow Allow from all </Proxy>
RewriteEngine on
RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P]
--nate
Hi Nate, Nope. There's no proxy configured. The only things I changed in the HTTP config part of the universe_wsgi.ini are the host and the port. Cheers, Chris Nate Coraor wrote:
Hi Chris,
It sounds like you maybe be running through a proxy, away from the server root, without the proxy-prefix option set in universe_wsgi.ini? If so, have a look at the documentation here:
http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy#Apacheconfigurationw...
--nate
Chris Cole wrote:
Hi,
I've been using the subversion version of Galaxy for a while, but now I want to update to the latest mercurial release.
I installed it in a new location as per the wiki and set-up the SGE settings as per my previous install and all the tests pass. It launches fine, but when viewing the website the frames seem to be off-by-one. i.e., the 'Tools' frame is empty except for "This link may not be followed from within Galaxy.", the tools are in the middle window and the 'History' frame has general information.
I can't see any errors in the paster.log file, so where can I look to sort out this error? Thanks,
Chris _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096
Chris, Could you send us your universe_wsgi.ini? We haven't seen this happen without a proxy before. --nate Chris Cole wrote:
Hi Nate,
Nope. There's no proxy configured. The only things I changed in the HTTP config part of the universe_wsgi.ini are the host and the port. Cheers,
Chris
Nate Coraor wrote:
Hi Chris,
It sounds like you maybe be running through a proxy, away from the server root, without the proxy-prefix option set in universe_wsgi.ini? If so, have a look at the documentation here:
http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy#Apacheconfigurationw...
--nate
Chris Cole wrote:
Hi,
I've been using the subversion version of Galaxy for a while, but now I want to update to the latest mercurial release.
I installed it in a new location as per the wiki and set-up the SGE settings as per my previous install and all the tests pass. It launches fine, but when viewing the website the frames seem to be off-by-one. i.e., the 'Tools' frame is empty except for "This link may not be followed from within Galaxy.", the tools are in the middle window and the 'History' frame has general information.
I can't see any errors in the paster.log file, so where can I look to sort out this error? Thanks,
Chris _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
participants (3)
-
Chris Cole -
Erick Antezana -
Nate Coraor