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gbrowse_cleanp - Online in the Cloud

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This is the command gbrowse_cleanp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



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
------ ---------
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.

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