May 29, 2017

The ungoogleable: Authenticating a Galaxy Portal with Active Directory

As a rule, Google is very useful for finding examples of how to configure software, especially when you're doing Unix-y stuff and using well worn programs like the Apache Web Server.  A recent configuration task I needed to perform was the exception that proved the rule: there is no working, non-trivial example on the Web of how to configure Apache to authenticate a user against an LDAP server that requires authentication to search (you don't want to hard code in a user name and password in the httpd.conf file, of course). Windows Active Directories often fall into this category, as they do not allow an anonymous search to start (Apache's default is an anon search, then bind with a user name, then search for attributes).

Specifically, the Galaxy Web server is a popular Python based bioinformatics package.  It uses Paster to serve up the Web pages, but expects you to put a user authentication proxy in front of it if you want to use CAS, LDAP, etc. to manage the portal's user accounts. Galaxy's Paster process then just blindly accepts the REMOTE_USER variable sent along by the proxy with each HTTP request. Ideally, the REMOTE_USER is a fully qualified e-mail address so that Galaxy can send e-mail notifications for features that have that capability e.g., notify a user when their analysis is complete. Kind of like this:

The keys to getting this to work are Apache's AuthLDAPInitialBindPattern and AuthLDAPRemoteUserAttribute directives. Feast your eyes on the following Apache config, that:
  1. takes a user name like "work_group_name\user_login_name"
  2. authenticates against an Active Directory with a long, complex binding DN like "CN=user_login_name,OU=work_group_name,OU=Users,OU=Accounts,DC=..."
  3. queries the user information in the directory for an e-mail address containing attribute (here userPrincipalName)
  4. forwards the e-mail address on to the paster Web server in the REMOTE_USER variable

# If the LDAP server cert is not chained with any of your root certs on the box and you can't import it
LDAPVerifyServerCert off
<VirtualHost my_proxy_site:443>
        ServerName my_proxy_site
        # Require SSL since the users will be entering their org credentials so we shouldn't accept them as plain-text
        SSLEngine on
        SSLCertificateFile /etc/ssl/certs/my_proxy_site.crt
        SSLCertificateKeyFile /etc/ssl/certs/my_proxy_site.key

        RewriteEngine On
        # Serve up static content directly rather than proxying, for efficiency
        RewriteRule ^/static/style/(.*) /opt/gls/galaxy/static/june_2007_style/blue/$1 [L]
        RewriteRule ^/static/scripts/(.*) /opt/galaxy/static/scripts/packed/$1 [L]
        RewriteRule ^/static/(.*) /opt/galaxy/static/$1 [L]
        RewriteRule ^/favicon.ico /opt/galaxy/static/favicon.ico [L]
        RewriteRule ^/robots.txt /opt/galaxy/static/robots.txt [L]
        # Send everything else through the proxy
        RewriteRule ^(.*) "http://the_web_server_expecting_remote_user_set:8080/$1" [P]

        <location "/">
        Order deny,allow
        Deny from all
        # We're picking specific subnets that are allowed to connect and authenticate
        Allow from 192.168.
        Allow from 10.0.0.

        # Authenticate against the org's Active Directory (one of three in this case)
        AuthName "Please login using your Organization_Name_Here credentials"
        AuthType Basic
        AuthBasicProvider ldap
        AuthLDAPURL "ldaps://ldap_server_name1 ldap_server_name2 ldap_server_name3/DC=my_suborg,DC=my_org,DC=my_tld?sAMAccountName,userPrincipalName?sub"
        AuthLDAPInitialBindAsUser on
        AuthLDAPInitialBindPattern (.+)\\(.+) CN=$2,OU=$1,OU=Users,OU=Accounts,DC=my_suborg,DC=my_org,DC=my_tld
        AuthLDAPRemoteUserAttribute userPrincipalName
        Require valid-user

        # Pass the LDAP account name we just authenticated on to the final destination (the Web server process at the_web_server_expecting_remote_user_set:8080) with the REMOTE_USER header set
        RewriteEngine On
        RewriteCond %{LA-U:REMOTE_USER} (.+)
        RewriteRule .* - [E=RU:%1]
        RequestHeader set REMOTE_USER %{RU}e



  1. Actually Galaxy don't need Apache or nginx to perform the LDAP authentication, see

  2. Hi Paul,

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