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.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.private) should be set to either
This file also specifies the paths to EMBOSS-related directories. You should ensure that you end directory names with a forward slash (
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:
To indicate whether Jemboss should run in client mode, connecting to a Jemboss server (as opposed to standalone mode):
The name of the public server; this will look like a URL:
The name of the private server; this will look like a URL:
The name of the service to connect to on the public server:
The name of the service to connect to on the private server:
Plplot graphics library directory (where the
*.fnt files are):
Location of EMBOSS data directory:
EMBOSS binary directory:
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:
Location of the acd directory in the EMBOSS installation:
URL for emboss application documentation (e.g.
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
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:
If you change any parameters relating to the client and you are using a web page launching method then you will need to rerun