RealPipelineTutorial should make use of variables to define reference.fa and MarkDuplicates.jar

[lonsbio]

From bjp...@unimelb.edu.au on 2012-02-07T17:39:04Z

https://code.google.com/p/bpipe/wiki/RealPipelineTutorial refers to reference.fa multiple times and uses an absolute path for MarkDuplicates.jar.

In both of these cases it might be valuable to assign them to variables at the top of the script.

It would create a single point of control and show the user how to use variables in their script.

Original issue: http://code.google.com/p/bpipe/issues/detail?id=8