7/17/13

HePCaT v1.0 Distribution README: Basic Installation Instructions

This distribution is freely available to academic users upon request.

U.S. Patent Pending, February 2013

Reference: PLOS Computational Biology (manuscript in press)

Contact: Jamie Wrabl (jowrabl@jhu.edu) or Vincent Hilser (hilser@jhu.edu)


1. Installation can be accompished on most Linux/Unix
   systems by following the instructions below.  (More
   detailed information can be found in the INSTALL file
   included in this distribution). 

   a. A ccp4 coordinate library is necessary for HePCaT to
      execute properly.  This library is included with the
      distribution.  To make this library, execute the 
      following commands:

      'cd ./HePCaT/src/mmdb109'
      './make mmdb'
      'sudo cp ./mmbd.a /usr/lib/libmmdb.a' OR
      'sudo cp ./mmbd.a /usr/lib64/libmmdb.a' (64-bit) 

   b. 'cd ./HePCaT/src' and execute './configure'

   c. Execute 'make' to compile the package.

   d. Description of command line arguments can be obtained
      by executing './HePCaT/src/hepcat' with no arguments.


2. HePCaT input files should contain only floating point numerical
   data, one datum per line.  Each line should end with a newline
   character.  An example is the following:

   10.067565
   12.445315
   15.010988
   11.212455
   
 
3. This software performs the data comparison but
   does not compute HePCaT P-values.  You must
   postprocess the output results with a software package
   of your choosing to integrate the appropriately
   parameterized InverseChiSquare distribution,
   as described in the manuscript text. A basic webserver
   that does compute P-values is available at: 
   http://best.bio.jhu.edu/HePCaT.


4. Please address comments and questions to:

   Jamie Wrabl (jowrabl@jhu.edu) or Vincent Hilser (hilser@jhu.edu)
   Johns Hopkins University Department of Biology