Gbrowse/authentication plugins/PamAuthenticate

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The PamAuthenticate plugin is one of a very small number of GBrowse Plugins that can be used to gather user credentials and authenticate them. This associates a user with a stable username and can be used to:

  1. Remember a user's preferences, uploads and other settings across multiple computers.
  2. Allow users to share tracks with each other and to make uploaded tracks public.
  3. Authorize certain users to access tracks and/or datasources.


The PamAuthenticate plugin is installed by default in /etc/gbrowse2/plugins, but is not activated. When activated, it uses the Pluggable Authentication Module (PAM) to authenticate users, and /etc/nsswitch.conf to associate users with groups. This allows considerable flexibility in connecting GBrowse to enterprise authentication/authorization backends, and allows you to use systems ranging in complexity from simple UNIX shadow files to complex Kerberos authentication systems.

Setting Up Username/Password Authentication

To set up the PamAuthenticate system, you need to configure a PAM service called "gbrowse" by creating the file /etc/pam.d/gbrowse. A simple /etc/pam.d/gbrowse file that uses local UNIX password/shadow databases would look like this:

auth     requisite

an LDAP-based authentication would refer to instead.

Note that if you are going to use the UNIX shadow password system for authentication, the web user must belong to the "shadow" group on many systems. You can arrange this as follows:

usermod -G shadow -a www-data

Change "shadow" and "www-data" to the group that can read the /etc/shadow file and the Apache user respectively. Note that you will typically not want to give server login privileges to all individuals who have genome browser accounts. You can use PAM to forbid actual logins to members of certain groups (see the module for more information).

Setting up Group Definitions

Pam authenticate.png

The PAM authentication plugin uses /etc/nsswitch.conf system configuration file to map users onto groups for group-based authentication. nsswitch.conf, in turn, provides connections to the traditional /etc/group file, the NIS database, or LDAP databases, depending on how it is configured. For example, to fetch user and group information from the local filesystem first, and then to look in LDAP, nsswitch.conf should have lines that looks like this:

passwd: compat ldap
group:  compat ldap

Once these steps are taken, you'll configure GBrowse to use the PAM authentication plugin. Edit /etc/gbrowse2/GBrowse.conf and add or uncomment the following line in the [GENERAL] section:

authentication plugin = PamAuthenticate

When you reload GBrowse, you will see a simple "Login" link in the upper right hand corner of the screen. Clicking on this link will bring up a dialog that prompts you for your login username and password. If all is configured correctly, then you'll be able to log in using your Unix username and password.

Customizing the Plugin

You can customize the messages that appear at the top and bottom of the login dialog box by setting configuration options in the [PamAuthenticate:plugin] stanza located in GBrowse.conf:

login hint = your UNIX account
login help = Please see your system administrator for help
if you have lost your password.
pam service name = gbrowse
login hint
This is the message that appears at the top of the dialog box, and is intended to be used to tell the user what credentials he is to supply. For example, you can change it to read "your Acme username and Cryptocard password".
login help
This is the message that appears at the bottom of the dialog box and is intended to provide contact information for the user if he cannot remember his password. It can contain HTML links if desired.
pam service name
This is the name of the pam.d service for gbrowse. You can place any defined service name in this option. For example, to use the PAM configuration for the login service, simply change the value to "login" and the same restrictions that are used for local logins (e.g. time of day) will be applied to GBrowse.

Further Information

For further information on how this plugin works, and some hints on how to create your own customized authentication plugin, please see Creating GBrowse Plugins.