I’m using Protégé for a class, and sadly the installer isn’t smart enough to install system-wide, which means I would have to cd to the install directory and issue ./run.sh to start protégé. Sub-optimal. Here’s the original run.sh:
#!/bin/sh
java ${CMD_OPTIONS} -Xmx200M -Dosgi.clean=true -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -jar org.eclipse.osgi.jar
And my better one:
#!/bin/bash
pushd /home/<myuser>/Protege_4.0_beta
java ${CMD_OPTIONS} -Xmx200M -Dosgi.clean=true -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -jar org.eclipse.osgi.jar
popd
This means that I can now go into my ~/bin and make a symlink to the run.sh as ‘protege’. Having done that, I can Alt-F2 and type ‘protege’ to start protege. Huzzah! Note that on some systems you may not have to replace sh with bash, but on Ubuntu sh is actually dash, which does not have pushd and popd.
Hopefully this will be useful to someone else installing Protégé on a Linux-based system.

