[EMBOSS] Jemboss Guide

[ajb at ebi.ac.uk]

The first thing to check is whether the programs work from
the command line. That will show whether any library
dependencies are missing. Remember that the
installed EMBOSS applications 'bin' directory must be in your PATH
for wossname to work properly from the command line.

The second thing to check is that the jembossctl application has
been properly made suid root e.g.:

-rwsr-xr-x 1 root users 44380 2008-02-09 11:11 jembossctl

If you installed Jemboss without using the installation script
(we recommend that you do use the script) then you should also
check your jemboss.properties file carefully. That lives in
      .../share/EMBOSS/jemboss/resources
and will look something like this for an installation in /usr/local/emboss
with SSL authentication activated:

user.auth=true
jemboss.server=true
server.public=https://1.2.3.4:8443/axis/services
server.private=https://1.2.3.4:8443/axis/services
service.public=JembossAuthServer
service.private=JembossAuthServer
plplot=/usr/local/emboss/share/EMBOSS/
embossData=/usr/local/emboss/share/EMBOSS/data/
embossBin=/usr/local/emboss/bin/
embossPath=/usr/bin/:/bin:/usr/local/bin
acdDirToParse=/usr/local/emboss/share/EMBOSS/acd/
embossURL=http://emboss.sourceforge.net/


> All I get is a window named Saved Results, which shows the command line
> generated. It's just wonderful that I can choose my font size and
> Plain/Bold/Italic for this window.

Thank you.

Alan