The Jemboss client and server use the file jemboss.properties as their primary source of setup 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 to install Jemboss in client-server mode or if you use the standalone Jemboss produced by an EMBOSS make install then this will have been automatically generated (.../share/EMBOSS/jemboss/resource/jemboss.properties) so you can skip this section. The information here is provided for completeness and for anyone wishing to customise the file.

Here is an example jemboss.properties file:

jemboss.server=true
user.auth=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.open-bio.org/rel/dev/apps/

The first line (user.auth=true) indicates that the server is expecting the user to login with a username and password.

The second line (jemboss.server=true) indicates you are using the Java JembossServer methods.

If you are using this file as a template then change 'localhost' in the above server names to be your IP address. The next lines (service.public and service.private) should be set to either JembossServer or JembossAuthServer.

This file also specifies the paths to EMBOSS-related directories. You should ensure that you end directory names with a forward slash (/).

Auto-generated jemboss.properties files can be found in the .../share/EMBOSS/jemboss/resource directory. Jemboss clients will read the properties file via the Java classpath. However, you may create a customised version of jemboss.properties in your home directory. If you do so then that file will be used by default.

jemboss.properties used by the client. An example jemboss.properties file that can be used by a Jemboss client to connect to a server that doesn't require user authorisation:

user.auth=false
jemboss.server=true
server.public=http://localhost:8080/axis/services
server.private=http://localhost:8080/axis/services
service.public=JembossServer
service.private=JembossServer
embossURL=http://emboss.open-bio.org/rel/dev/apps/

jemboss.properties used by the server. An example jemboss.properties file that can be used by a Jemboss server that doesn't require user authorisation:

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. To indicate that the server is not (if false) expecting any user authentication:

user.auth=false

To indicate whether Jemboss should run in client mode, connecting to a Jemboss server (as opposed to standalone mode):

jemboss.server=true

The name of the public server; this will look like a URL:

server.public

The name of the private server; this will look like a URL:

server.private

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

service.public

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

service.private

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

plplot

Location of EMBOSS data directory:

embossData

EMBOSS binary directory:

embossBin

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:

embossPath

Location of the acd directory in the EMBOSS installation:

acdDirToParse

URL for emboss application documentation (e.g. http://emboss.open-bio.org/rel/dev/apps/):

embossURL

It is possible for Jemboss to get the application help from the Jemboss server. This can be done using a blank entry for this property in jemboss.properties i.e.:

embossURL=

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

Other environment variables for running emboss:

embossEnvironment

For example:

embossEnvironment=OMP_NUM_THREADS=4 LD_LIBRARY_PATH=/usr/local/lib