# Un-pack the tar-ball: 

tar -xvzf Platypus_0.1.5.tgz

# Build pysam first:

cd PlatypusRelease/pysam
python2.6 setup.py install --prefix=PATH_TO_INSTALL_PLATYPUS_LIBRARIES

# Then build Platypus

cd PlatypusRelease/
python2.6 setup.py install --prefix=PATH_TO_INSTALL_PLATYPUS_LIBRARIES

# To run Platypus, the path you installed the libraries to must be in your $PYTHONPATH environment variable, so you need
# to set that:

export PYTHONPATH=$PYTHONPATH:PATH_TO_INSTALL_PLATYPUS_LIBRARIES

# The you should be able to run Platypus. It takes BAM and a reference FASTA file as input, and outputs VCF. Each BAM is treated
# as a separate sample. Here is an example of how to run Platypus:

python2.6 Platypus.py callVariants --bamFiles=LIST_OF_BAMS --refFile=REF.fa --regions=chr20:0-1000000 --output=Calls.vcf


You can see a list of all the possible input options by running the following comand:
python2.6 Platypus.py callVariants --help