Complete online documentation can be found at
https://wiki-bsse.ethz.ch/display/ShoRAH/Installation


REQUIREMENTS
------------

***Languages***

ShoRAH is a collection of programs written in C, C++ (for which you will need a compiler),
Python (version 2.6 or later, but not Python 3.x) and Perl. They come with almost any
distribution of Linux and Mac OS X, or they can be downloaded and installed.


***Libraries***

Please download and install:

- Biopython (http://biopython.org/wiki/Download), following the online instructions.
- GSL (GNU scientific library) from http://www.gnu.org/software/gsl/, installation is
  described in the included README and INSTALL files.
- needle, a program found in EMBOSS (http://emboss.sourceforge.net/) is needed for the
  alignment step. Install EMBOSS and make sure needle is in your path, or place an alias.


INSTALLATION
------------

Download and extract the gzipped tar archive (shorah-0.x.tar.gz). Change to the
extracted directory, and then to the samtools directory. Run make. Then change 
back to the extracted directory, and run make again.

Running make should be sufficient in most cases. In case
the gsl library is not located in the standard location,
you may have to edit the lines indicated in Makefile.


ISSUES
------
- Check if the issue has been reported on http://wiki-bsse.ethz.ch/display/ShoRAH/Getting+help
- Contact your administrator (it might be something easy)
- Contact us: shorah@bsse.ethz.ch