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

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

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