The Jemboss client and server use jemboss.properties to determine information. The client uses this file to determine the name and location of the server. The server uses this file to define where EMBOSS is installed. If you used the install-jemboss-server.sh script then this should have been automatically generated ($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties). This is an example:

user.auth=true
jemboss.server=true
server.public=https://localhost:8443/axis/services
server.private=https://localhost: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:/packages/clustal/:/packages/primer3/bin:
acdDirToParse=/usr/local/emboss/share/EMBOSS/acd/
embossURL=http://emboss.sourceforge.net/apps/
 

The first line (user.auth=true) indicates that the server is expecting the user to login.
The second line (jemboss.server=true) indicates you are using the Java JembossServer methods.
Change 'localhost' in the above server names to your ip address.
The next lines (service.public and service.private) must be exactly the same as the ID name used to deploy the services.

Also, make sure the above have the correct paths to EMBOSS (and ensure you end the path name with a forward slash '/'!).

The jemboss.properties file, in the case of the server, should be read from the $EMBOSS_ROOT/share/EMBOSS/jemboss/resource directory in the distribution. The client will read the properies file from the classpath (so this can be set as a default in the distribution of the client) or from the users home directory. For example, the client downloaded from the HGMP Jemboss launch site sets the defaults to the HGMP server. However, this can be overridden by putting an alternative jemboss.properties for it to read in the user's home directory.

jemboss.properties used by the client

user.auth=false
jemboss.server=true
server.public=http://localhost:8080/axis/services
server.private=http://localhost:8080/axis/services
service.public=JembossAuthServer
service.private=JembossAuthServer
embossURL=http://emboss.sourceforge.net/apps/

jemboss.properties used by the server

user.auth=false
plplot=/usr/local/emboss/share/EMBOSS/
embossData=/usr/local/emboss/share/EMBOSS/data/
embossBin=/usr/local/emboss/bin/
embossPath=/usr/bin/:/bin:/packages/clustal/:/packages/primer3/bin:
acdDirToParse=/usr/local/emboss/share/EMBOSS/acd/

jemboss.properties Definitions

jemboss.server=true

Indicates if you are using the JembossServer methods (set to true) or the HGMP cgi private server (set to false). It is likely then that this should always be true.

server.public

The name of the public server, this will look like a URL.

server.private

The name of the private server, this will look like a URL.

service.public

The name of the service to connect to on the public server.

service.private

The name of the service to connect to on the private server.

plplot

plplot graphics library directory (where the *.fnt files are).

embossData

location of data read by EMBOSS.

embossBin

EMBOSS binary directory.

embossPath

Path used in the environment to run the EMBOSS applications. There are applications that may need to be added to the path such as clustalw and primer3_core. Also, if 'emboss.default' is set up to use SRS to retrieve sequences from databases, the path to 'getz' should be added.

acdDirToParse

location of the acd directory in the EMBOSS distribution.

embossURL

URL for emboss application documentation (e.g. http://emboss.sourceforge.net/apps/). It is possible for Jemboss to get the application help from the Jemboss server if so desired. This can be done using a blank entry for this property in jemboss.properties:

embossURL=

It will then not use a URL but get the Jemboss server to run 'tfm' to retrieve the help.

embossEnvironment

Other environment variables for running emboss. For example:
embossEnvironment=OMP_NUM_THREADS=4 LD_LIBRARY_PATH=/usr/local/lib