NAME¶

gbrowse_clean.pl - Clean up sessions and other temporary gbrowse2 files

SYNOPSIS¶

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

OPTIONS¶

-verbose

Report actions verbosely, printing out each session, file and directory deleted.

-help

Print a brief help message and exits.

-man

Prints the manual page and exits.

DESCRIPTION¶

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
 ------     ---------
  s         seconds
  m         minutes
  h         hours
  d         days
  w         weeks
  M         months
  y         years

expire session 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 his session, so simply loading a region in the browser without changing settings is sufficient to prevent a session from expiring.

expire cache 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.

expire uploads 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 point.

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.

AUTHOR¶

Lincoln D. Stein <lincoln.stein@gmail.com> 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.

SEE ALSO¶

<http://gmod.org/wiki/GBrowse_2.0_HOWTO>