[EMBOSS] Making Jemboss available to all

simon andrews (BI) simon.andrews at bbsrc.ac.uk
Wed Jan 21 15:01:34 UTC 2004

> -----Original Message-----
> From: Dr T. Carver [mailto:tcarver at rfcgr.mrc.ac.uk] 
> Subject: Re: [EMBOSS] Making Jemboss available to all

Tim - thanks for the reply.

> This isn't a problem I have encountered before.
> It may be useful if you provided the script.

The launch script I'm using is just the standard jemboss.bat launch script which is included in the Jemboss download package.  I'm linking to this script using a windows shortcut.

The reason this doesn't just work is that when you create the shortcut it asks for a target and a "start in" directory.  The target is no problem, but I can't use a UNC path as the directory to start in.  This appears to be a limitation of the MS cmd shell:

C:\>cd \\server\share
CMD does not support UNC paths as current directories.

This then causes the jemboss.bat to fail as it includes the line:

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

Because the Jemboss directory isn't the same as ".", the classpath statement fails and Jemboss with the error 

"Program could not find the main class.  Program will exit"

I've tried substituting the . in the classpath for the full UNC path, and whilst this doesn't itself throw an error I still get the same error message as before when I try to run it.  From the little information I've found it appears that the JRE itself doesn't allow UNC paths in a classpath statement (I'm not 100% sure about this though).

As I said before, if I map \\server\share to X: then I can successfully run Jemboss either from a shortcut directly, or indirectly using X:\Jemboss\ in the classpath.  This isn't an option sitewide though as there isn't a drive letter I can guarantee will be free.

> An alternative of course is just to set up a web launch page:

I've looked at that and that seems to be one way around this.  The problem with this is that our site standard image currently doesn't include Java Web Start so I'd have to get that installed first.  It would also mean that Jemboss wouldn't appear with all the other applications we've got set up.

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