gbrowse_clean.pl - Clean up sessions and other temporary gbrowse2 files
From the command line:
sudo -u www-data gbrowse_clean.pl
Replace "www-data" with the web server account name on your system.
To run automatically under cron, create a crontab file for the web server user
that contains a line like the following:
# m h dom mon dow command
5 0 * * /usr/bin/gbrowse_clean.pl >>/var/log/gbrowse2/gbrowse_clean.log
- Report actions verbosely, printing out each session, file
and directory deleted.
- Print a brief help message and exits.
- Prints the manual page and exits.
GBrowse2 generates a number of temporary files during its operations. These
files include session data, data cache files, and temporary image files, as
well as user upload data from custom tracks.
This script expires these temporary files, releasing unneeded space. The script
honors the following options from the GBrowse.conf master configuration file:
Name Default Description
---- ------- -----------
exire session 1M How long to keep session data
expire cache 2h How long to keep cache data
expire uploads 6w How long to keep user track data
Time intervals are indicated using a count and a unit:
Suffix Time Unit
controls how long before user session data expires. Once a
session expires, the user's saved settings, such as his preferred data source,
track visibility settings, and custom track uploads are purged. The expiration
interval is measured since the last time the user accessed
so simply loading a region in the browser without changing settings is
sufficient to prevent a session from expiring.
controls how long before cached track data is purged from
the system. Caching for up to a few hours increases performance because users
frequently reload the same region. Caching for longer periods increases the
time between updating the database and tracks displaying those changes.
controls how long to keep user uploaded data for custom
tracks on disk. It makes sense to keep it on disk for as long or longer than
the session. Even if the user's session expires, he can still get at the
uploaded data if he bookmarked his session or shared the uploaded track at any
This script should be run periodically, ideally under cron. Once per day should
be adequate for most uses, but heavily-used sites may wish to run the script
more frequently. It is important to run the script under the same user account
as the web server; otherwise the script will be unable to delete the files
created by the web server user during gbrowse execution. Do not run this
script as root.
Lincoln D. Stein <firstname.lastname@example.org> Copyright 2009 Ontario
Institute for Cancer Research
This script is available under either the GNU General Public License or the Perl
Artistic License version 2.0. See LICENSE in the GBrowse source code
distribution for details.