Prerequisites
Before installing PFMS make sure the following programs are installed:
Python 2.6 or a higher version
GCC or a C compiler
Perl (Required to use SISSRs peak-finder)
JRE 1.6 (Required to use FindPeaks peak-finder) and to handle a dataset containing reads of more than one chromosome
Note: PFMS localy installs the included peak finders, BEDTools 2.16.2 and samtools .
Installation
1. Get the latest version of PFMS from 'Download' section
2. Extract the downloaded package:
unzip -q PFMS-1.3.zip
3. PFMS can either be installed in standard Python application directory of the operating system (for users with root access) or any directory under users' home (for users unable to install programs due to authenticity issues).
3.1 Standard installation:
Open a terminal, change the current directory to the extracted directory (aka. PFMS-1.3) and type:
sudo python setup.py install
Or
3.2 Standalone installation (hint: the scripts can only be executed in the extracted directory)
Open a terminal, change the current directory to the extracted directory (aka. PFMS-1.3) and type:
python setup.py install -normal
