How to logout after starting the web interface of Pathway Tools

The Pathway Tools web interface requires an X-server. If the user who is running the web interface needs to log out while the web interface is running, then you need a terminal and an X-Server that can run while nobody is logged in. Setting up such a terminal and X-Server and setting up the Pathway Tools web interface to use them can be quite time-consuming and probably requires the help of a SysAdmin.

One such X-Server, the one we use, is a Unix program called Xvfb, which is freely available on the web. Choose an X display number greater than zero. We use display 1. Your SysAdmin will have to set up permissions for the account that runs the web interface to write to the X-Server's files, which, on our Suns, are at /tmp/.X11-pipe/Xn and /tmp/.X11-unix/Xn, where n is the display number you chose. We use GNU screen so that the web interface has a place to send its diagnostic output, and I suggest you do the same. Xvfb and GNU screen are started from our custom startup script, which you can modify for your needs:

#!/bin/csh
# Warn and exit if something is already listening on port 1555.
if (`netstat -a | fgrep 1555 | fgrep -c LISTEN` == 1) then
  echo Something is already listening on port 1555.
  echo Please stop whatever it is, and then try $0 again.
  exit
endif
# Start Xvfb as X-server display #1. If it's already been started, no harm done.
# This works in conjunction with the pathway-tools script which needs to have the
# environment variable DISPLAY defined - the setenv is necessary to make sure the
# binding is inherited by subsequent scripts (like pathway-tools):

setenv DISPLAY :1
/home/Xvfb $DISPLAY > & /dev/null &

# Start GNU screen (hit Ctrl-A Ctrl-D to detach). Within it, start Pathway Tools.

screen -m -d /home/aic-export/pathway-tools/ptools/[version]/pathway-tools -www -www-publish all

As indicated in the comments in the script above, you don't need to modify the pathway-tools script if you use this script. You can modify the binding of DISPLAY above if you'd rather a different display port were used.

• what is screen, and how do i use it?
• GNU screen quick reference
• Linux Forum on GNU screen
• Screen Command Examples

If you need additional help getting this to work, send email to .