[EMBOSS] jemboss rebase etc can't utilize embossre.enz file

[John Marken]

Thank you. There indeed was another copy of jemboss.properties in the home directory for the tomcat server owner. And it actually is important to not install  the server as root:>)

John
-----Original Message-----
From: Dr T. Carver [mailto:tcarver at rfcgr.mrc.ac.uk]
Sent: Friday, February 27, 2004 2:25 AM
To: John Marken
Subject: Re: [EMBOSS] jemboss rebase etc can't utilize embossre.enz file


Hi John

This looks to be the correct jemboss.properties (just ensure there isn't
one in the home directory of the tomcat user).

Did you run 'rebaseextract'?

What does the rest of the jemboss.properties look like?

Regards
Tim

Tim Carver
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500  Fax: +44 1223 494512
E-mail: tcarver at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk


On Thu, 26 Feb 2004, John Marken wrote:

> Hello,
> Just installed jemboss, the interface works but programs needing database files like remap don't work. Remap can return the sequence and translations but no restriction enzyme sites are shown, nor are there enzymes listed the cuts or no cut sections of the resulting file. Command line emboss is working and  remap can find the rebase (embossre.enz etc)  files as specified in the .embossrc in //usr/local/emboss/share/EMBOSS/data/REBASE.
>
> The jemboss.properties file in
> "//usr/local/jakarta-tomcat-4.1.29/webapps/axis/WEB-INF/classes/resources"
> contains the line
> "embossData=/usr/local/emboss/share/EMBOSS/data/" (without quotes)
>
> Is the jemboss.propterties file in the right place? Is there another config file that needs editing?
>
> Regards
> John Marken
>
>
> Trubion Pharmaceuticals Inc.
> 2401 4th Ave. Suite 1050
> Seattle, WA 98121
> 206-838-0500
>
>