[EMBOSS] Solved: Making Jemboss available to all

simon andrews (BI) simon.andrews at bbsrc.ac.uk
Thu Jan 22 10:01:45 UTC 2004

Following a series of helpful emails from Tim Carver at RFCGR I've now managed to set up the Jemboss client so that it's accessible to a whole site from a Windows network share.  If anyone is interested in doing this in the future I thought I'd summarise how I did it.

These instructions detail how you would install Jemboss onto \\server\share

First, download the Jemboss client from:


Create the directory \\server\share\Jemboss and unzip the downloaded file into there.

Open \\server\share\Jemboss\jemboss.bat in a text editor

You need to edit the line which starts:

start javaw -classpath .;Jemboss.jar;JembossAlignment.jar;axis.jar...

You need to change the initial . to \\server\share\Jemboss and then prefix each of the xxxx.jar entries with \\server\share\Jemboss\ .  The only entry you don't need to prefix is the very last one which defines the first class to launch.  You will end up with a very long command which looks something like this:

start javaw -classpath \\server\share\Jemboss;\\server\share\Jemboss\Jemboss.jar; ..snip.. \\server\share\Jemboss\grout.jar org.emboss.jemboss.Jemboss

You now need to make the directory \\server\share\Jemboss\resources and copy into it an appropriate jemboss.properties file to connect to your Jemboss server.  Details of how to construct the jemboss.properties file can be found here:


Finally, to run the program easily you can create a shortcut to the jemboss.bat file.  It's also a good idea when creating the shortcut to go into its properties and under the Shortcut tab change the Run variable to "Minimised".  If you don't do this you get a brief flash of a DOS window when you launch Jemboss, and then a wait until the first jemboss window appears.  We found that our users got impatient in this time and clicked the link again.

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