If you want to run Picard's Mark Duplicates on Lonestar, do roughly this:
The output metrics file is required and worth screening before you go further.
Picard is also installed on fourierseq at /usr/local/genome/bin and the jar files are in fourierseq user's paths.
General syntax for using picard jar files:
java -Xmx4g -jar /usr/local/genome/bin/jarfilename
Find picard document here