#Platypus

The Platypus variant caller. The main Web site is https://github.com/andyrimmer/Platypus.

##Installation and execution

To build Platypus, do the following:

make

Then to run do

python bin/Platypus.py --bamFiles=BAM.bam --refFile=REF.fa --output=variants.vcf

Platypus has been tested with Python 2.6 and 2.7, and requires Cython 0.20.2 or later to build.

####Prerequisites

Platypus requires HTSlib 1.2.1 or greater. HTSlib can be downloaded from the HTSlib Web site.

To build and install HTSlib, cd into HTSlib source and type make install. This will install HTSlib under /usr/local/ (see note below). To install HTSlib in any other directory use make install prefix=/path/to/dir.

NOTE: HTSlib should be installed in a standard location (e.g. /usr/local/). If not installed in a standard location, you will need to set your library paths:

For GNU/Linux:

export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib (only for making)
export LD_LIBRARY_PATH=/path/to/dir/lib

Note the /include and /lib sub-directories. e.g. if you installed HTSlib under /Users/me/htslib then set

export C_INCLUDE_PATH=/Users/me/htslib/include
export LIBRARY_PATH=/Users/me/htslib/lib
export LD_LIBRARY_PATH=/Users/me/htslib/lib

HTSlib will automatically make the include and lib directories on install.

For OSX:

export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib (only for making)
export DYLD_FALLBACK_LIBRARY_PATH=/path/to/dir/lib