Common Problems with GBrowse2 Installation

Here are some common problems.

GBrowse loads, but the fonts and colors are wrong, and none of the click or drag options works.

This happens when GBrowse can't find its css and/or javascript files. To confirm, check the server error log. You will see messages about missing .css and .js files. Check and correct the url_base setting in GBrowse.conf. This can sometimes happen when you tell the installer to put GBrowse's htdocs files in a non-standard location.

When upgrading from an earlier version of GBrowse2, you get an "Internal Server Error" message and the server error log complains about a "Deparse" error.

This is caused by the GBrowse2 config file parsing and caching system, which speeds up loading of large config files. Perl can't correctly cache certain complex callbacks. To fix this problem, try to isolate which callback(s) are causing the problem and rewrite them to be standard sub {} callbacks. If nothing else works, edit the Apache config file to set the environment variable GBROWSE_NOCACHE to a true value (such as "1") and restart the server. This will disable the caching system.

More information on this: for standard CGI installs, find the Apache config file that contains GBrowse configuration information (often in /etc/apache2/conf.d/gbrowse2.conf), and add a SetEnv directive. E.g.

<Directory "/usr/lib/cgi-bin/gb2">
 SetEnv GBROWSE_NOCACHE "1"
 SetEnv GBROWSE_CONF   "/etc/gbrowse2"  # this should already be there
</Directory>

For mod_fcgid:

DefaultInitEnv GBROWSE_NOCACHE "1"

For mod_fastcgi:

FastCGIConfig -initial-env GBROWSE_NOCACHE=1