We also ran into this. Our local server configuration was case-sensitive and the LDAP uid key was converted to upper-case, so we used:

RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e

which fixed the problem. We found the solution by searching for 'AUTHENTICATE_uid', it appears to be a relatively common thing.

Beyond that everything else was the same from the Galaxy wiki.

chris

On Jan 19, 2012, at 8:19 AM, Langhorst, Brad wrote:

Hi Sarah:

I don't know what kind of LDAP you're talking to... I'm talking to Active Directory and this configuration works in that situation.

Order allow,deny allow from all

           AuthType Basic
           AuthName "NEB Credentials"
           AuthBasicProvider ldap
           AuthzLDAPAuthoritative off
           AuthLDAPBindDN ccalookup@neb.com
           AuthLDAPBindPassword <password>
           AuthLDAPURL

"ldap://<ldap.domain.com>:389/dc=domain,dc=com?sAMAccountName" require valid-user

           RewriteCond %{IS_SUBREQ} ^false$
           RewriteCond %{LA-U:REMOTE_USER} (.+)
           RewriteRule . - [E=RU:%1]
           RequestHeader set REMOTE_USER

%{AUTHENTICATE_sAMAccountName}e

-- Brad Langhorst New England Biolabs langhorst@neb.com

On 1/19/12 8:59 AM, "Sarah Maman" sarah.maman@toulouse.inra.fr wrote:

...

Hello,

I'm trying to install galaxy on a apache server,and i have the same error message than David HOOVER when i tried to generate the authentification files. Thanks to David Hoover who gives me some helpful explanation.

When i read the thread on gmod, it seems,that the problem is solved (http://gmod.827538.n3.nabble.com/trouble-with-authentication-through-Apac he-td1809681.html http://gmod.827538.n3.nabble.com/trouble-with-authentication-through-Apac he-td1809681.html) but I did not find the solution in my case.

I use LDAP authentification and Galaxy is implemented on a VM.

Could you please explain me how to solve it. I really need help.

I modified universe file ( in galaxy-dist) and i created .htaccess file in galaxy-dist/ :

• in universe_wsgi.ini:

use_remote_user = True remote_user_maildomain = example.org http://example.org

• in .htaccess file in galaxy-dist/ Directory :

1 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_1 # Define Galaxy as a valid Proxy 2 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_2 <Proxy http://localhost:8080%3E 3 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_3 Order deny,allow 4 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_4 Allow from all 5 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_5 </Proxy> 6 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_6 #!highlight apache 7 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_7 <Location "/"> 8 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_8 AuthType Basic 9 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_9 AuthBasicProvider *ldap* 10 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_10 Auth*LDAP*URL "*ldap*://server:389/ou=People,dc=example,dc=org?uid?sub?(objectClass=pers on)" 11 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_11 Authz*LDAP*Authoritative off 12 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_12 Require valid-user 13 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_13 # Set the REMOTE_USER header to the contents of the *LDAP* query response's "uid" attribute 14 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_14 RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e 15 http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%2 9#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_15 </Location>

with location, AuthBasicProvider and proxy competed

But i have the error :

Access to Galaxy is denied

Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server.

Thank you, and best regards

Sarah Maman

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Why do you need to create a proxy? The way I have ours set up is within a virtual host:

<VirtualHost>

<Location "/"> AuthName "Helix Systems" AuthType Basic AuthBasicProvider ldap AuthzLDAPAuthoritative off AuthLDAPUrl ldaps://helixdrive.nih.gov/ou=Users,ou=helix.nih.gov,o=scb?uid AuthLDAPBindDN "cn=maccount,ou=Special,o=scb" AuthLDAPBindPassword ******** Require valid-user RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e Options None Order Allow,Deny Allow from all </Location>

RewriteRule ^/static/style/(.*) /data/galaxy/pro/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /data/galaxy/pro/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /data/galaxy/pro/static/$1 [L] RewriteRule ^/favicon.ico /data/galaxy/pro/static/favicon.ico [L] RewriteRule ^/robots.txt /data/galaxy/pro/static/robots.txt [L] RewriteRule ^(.*) http://helixweb4.cit.nih.gov:8080$1 [P]

</VirtualHost>

David

On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote:

Hi Brad, Hi Christopher,

Thanks a lot. I'm talking to Open LDAP. I have changed

RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e to RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e

But I always have the same message /(Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. )/

This is my .conf file : <Proxy http://localhost:8080%3E Order deny,allow Allow from all </Proxy>

  RewriteEngine on

  <Location "/">
          AuthType Basic
          AuthName Galaxy
          AuthBasicProvider ldap
          AuthLDAPURL "ldap://server/ou=People,ou=genopole,ou=toulouse,o=inra,c=fr?u

id?sub?(objectClass=person)" AuthzLDAPAuthoritative off Require valid-user # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. #RewriteCond %{IS_SUBREQ} ^false$ #RewriteCond %{LA-U:REMOTE_USER} (.+) #RewriteRule . - [E=RU:%1] #RequestHeader set REMOTE_USER %{RU}e RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e </Location>

Thanks in advance, Sarah

Langhorst, Brad a écrit :

...

Hi Sarah:

I don't know what kind of LDAP you're talking to... I'm talking to Active Directory and this configuration works in that situation.

Order allow,deny allow from all

           AuthType Basic
           AuthName "NEB Credentials"
           AuthBasicProvider ldap
           AuthzLDAPAuthoritative off
           AuthLDAPBindDN ccalookup@neb.com
           AuthLDAPBindPassword <password>
           AuthLDAPURL

"ldap://<ldap.domain.com>:389/dc=domain,dc=com?sAMAccountName" require valid-user RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e

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David,

This is the approach recommended on the wiki for performance:

http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy

Would be nice if your alternative approach using virtual hosts were similarly documented.

chris

On Jan 19, 2012, at 10:01 AM, David Hoover wrote:

Why do you need to create a proxy? The way I have ours set up is within a virtual host:

<VirtualHost>

<Location "/"> AuthName "Helix Systems" AuthType Basic AuthBasicProvider ldap AuthzLDAPAuthoritative off AuthLDAPUrl ldaps://helixdrive.nih.gov/ou=Users,ou=helix.nih.gov,o=scb?uid AuthLDAPBindDN "cn=maccount,ou=Special,o=scb" AuthLDAPBindPassword ******** Require valid-user RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e Options None Order Allow,Deny Allow from all

</Location>

RewriteRule ^/static/style/(.*) /data/galaxy/pro/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /data/galaxy/pro/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /data/galaxy/pro/static/$1 [L] RewriteRule ^/favicon.ico /data/galaxy/pro/static/favicon.ico [L] RewriteRule ^/robots.txt /data/galaxy/pro/static/robots.txt [L] RewriteRule ^(.*) http://helixweb4.cit.nih.gov:8080$1 [P]

</VirtualHost>

David

On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote:

...

Hi Brad, Hi Christopher,

Thanks a lot. I'm talking to Open LDAP. I have changed

RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e to RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e

But I always have the same message /(Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. )/

This is my .conf file : <Proxy http://localhost:8080%3E Order deny,allow Allow from all </Proxy>

 RewriteEngine on

 <Location "/">
         AuthType Basic
         AuthName Galaxy
         AuthBasicProvider ldap
         AuthLDAPURL "ldap://server/ou=People,ou=genopole,ou=toulouse,o=inra,c=fr?u

id?sub?(objectClass=person)" AuthzLDAPAuthoritative off Require valid-user # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. #RewriteCond %{IS_SUBREQ} ^false$ #RewriteCond %{LA-U:REMOTE_USER} (.+) #RewriteRule . - [E=RU:%1] #RequestHeader set REMOTE_USER %{RU}e RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e </Location>

Thanks in advance, Sarah

Langhorst, Brad a écrit :

...

Hi Sarah:

I don't know what kind of LDAP you're talking to... I'm talking to Active Directory and this configuration works in that situation.

Order allow,deny allow from all

          AuthType Basic
          AuthName "NEB Credentials"
          AuthBasicProvider ldap
          AuthzLDAPAuthoritative off
          AuthLDAPBindDN ccalookup@neb.com
          AuthLDAPBindPassword <password>
          AuthLDAPURL

"ldap://<ldap.domain.com>:389/dc=domain,dc=com?sAMAccountName" require valid-user RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e

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Hi,

Thanks to log messages from remoteuser.py in "./lib/galaxy/web/framework/middleware/remoteuser.py":

print('affichage des variables d acces')

print ('self domain : %s'%self.maildomain)

print ('path info : %s'%path_info)

print ('admin user : %s' %self.admin_users)

http_remote_user = environ.get('HTTP_REMOTE_USER','')

print ('http remote user : %s'%http_remote_user)

remote_user = environ.get('REMOTE_USER', '')

print ('remote user :%s' %remote_user)

Galaxy prints every environment variable it receives, and I have seen that HTTP_REMOTE_USER variable is "(null)".

Moreover, Galaxy is defined as a valid Proxy (reverse proxy ??) so galaxy.conf is :

<VirtualHost localhost:port> # Define Galaxy as a valid Proxy <Proxy localhost:port> Order deny,allow Allow from all RewriteEngine on # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] # Set the REMOTE_USER header to the contents of the LDAP query response's "uid" attribute RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e

RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/static/style/(.*) /usr/local/bioinfo/src/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/(.*) /usr/local/bioinfo/src/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/images/(.*) /usr/local/bioinfo/src/galaxy/galaxy-dist/static/images/$1 [L] RewriteRule ^/favicon.ico /usr/local/bioinfo/src/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/favicon.ico /var/www/html/favicon.ico [L] RewriteRule ^/robots.txt /usr/local/bioinfo/src/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) localhost:port$1 [P]

</Proxy>

<Location "/....." > AuthType Basic AuthBasicProvider ldap AuthName "Galaxy" AuthLDAPURL "ldap://serveur ..." AuthzLDAPAuthoritative on

Require valid-user </Location>

</VirtualHost>

But, I didn't achieve, yet , to access REMOTE_USER value throught proxy.

In universe_wsgi.ini,

*use_remote_user = True*

and

*remote_user_maildomain = toulouse.inra.fr*

Thanks in advance, Sarah

Nate Coraor a écrit :

On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote:

...

Hi Brad, Hi Christopher,

Thanks a lot. I'm talking to Open LDAP. I have changed

RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e to RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e

But I always have the same message /(Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. )/

Hi Sarah,

This configuration will need to be in your Apache config (the location of which varies depending on your OS and/or how Apache is installed) rather than an .htaccess file.

--nate

...

This is my .conf file : <Proxy http://localhost:8080%3E Order deny,allow Allow from all </Proxy>

  RewriteEngine on

  <Location "/">
          AuthType Basic
          AuthName Galaxy
          AuthBasicProvider ldap
          AuthLDAPURL "ldap://server/ou=People,ou=genopole,ou=toulouse,o=inra,c=fr?u

id?sub?(objectClass=person)" AuthzLDAPAuthoritative off Require valid-user # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. #RewriteCond %{IS_SUBREQ} ^false$ #RewriteCond %{LA-U:REMOTE_USER} (.+) #RewriteRule . - [E=RU:%1] #RequestHeader set REMOTE_USER %{RU}e RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e </Location>

Thanks in advance, Sarah

Langhorst, Brad a écrit :

...

Hi Sarah:

I don't know what kind of LDAP you're talking to... I'm talking to Active Directory and this configuration works in that situation.

Order allow,deny allow from all

           AuthType Basic
           AuthName "NEB Credentials"
           AuthBasicProvider ldap
           AuthzLDAPAuthoritative off
           AuthLDAPBindDN ccalookup@neb.com
           AuthLDAPBindPassword <password>
           AuthLDAPURL

"ldap://<ldap.domain.com>:389/dc=domain,dc=com?sAMAccountName" require valid-user RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e

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