This method of setting up Jemboss is designed for local copies of EMBOSS on either a workstation or laptop. From EMBOSS 6.1.0 onwards an installation of the main EMBOSS package (Chapter 1, Building EMBOSS) will automatically configure a standalone version of Jemboss.
A UNIX workstation or laptop
SUN Java JDK or JRE from http://java.sun.com, or OpenJDK.
A fresh unpacking of the EMBOSS source code i.e. remove all existing versions.
PNG graphics (see platform-specific notes (Section 1.7, “EMBOSS Installation: Platform-specific Concerns”) in the EMBOSS installation instructions.)
At the time of writing the following software versions are current and will work with Jemboss. For the lifetime of the project we will, as far as possible, make Jemboss compatible with the latest stable Java releases.
Java 6 JDK
OpenJDK 6
All you need to do is to follow the instructions for compiling the main EMBOSS package (Chapter 1, Building EMBOSS). However, you must have ended up installing it using a make install command. As well as installing the EMBOSS binaries to the bin installation subdirectory this will also create a script for running the standalone Jemboss. The script is called runJemboss.csh and can be run, by name, just like any other EMBOSS application or UNIX system command.
As long as you have followed the instructions for the post-installation of the main EMBOSS package (Section 1.6, “Post-installation of EMBOSS”), with particular reference to correctly setting the PATH, then no further post-installation should be required.