[galaxy-dev] Executing a binary file from Galaxy job

Hi, I have a perl script which executes a Java JAR file located in tool-data/shared/jars/ and this Jar file at one point executes 2 other binary programs during its job process. These 2 programs are located in the same directory as the JAR file.

I am getting errors in Galaxy saying "No such file or directory" when these 2 external programs are called. I am assuming this is the case because they are not located in current working directory of the current Galaxy job process.

Is there a way to somehow redirect Galaxy into the correct directory where the binary files are located?

Thanks.