TOPICS:

1. REQUIREMENTS
2. INSTALLATION (short version)
3. FURTHER INFORMATION
4. LICENCE

0. LICENCE

IMPORTANT: THIS SOFTWARE PACKAGE CONTAINS TWO PIECES OF SOFTWARE. EACH PIECE OF SOFTWARE HAS A DIFFERENT AUTHOR.

Finestructure (fs v2.1) is free for Academic Use Only, under the terms included as LICENSE-FS. fs (finestructure) is written by Daniel Lawson (dan.lawson@bristol.ac.uk). 

ChromoPainter (fs cp) is also free for Academic Use Only, under the terms included as LICENSE-CP. ChromoPainter (the tool called by fs cp and used by fs) is written by Garrett Hellenthal (ghellenthal@googlemail.com).

They are included together for convenience only. THEY ARE SEPARATELY LICENCED PIECES OF SOFTWARE. Both licences allow the same use, and are free for academic use.

Read the COPYING file for details.

1. REQUIREMENTS

Assuming that you are in a Linux environment, you need:
1. an up-to-date version of the gcc compiler, e.g. "gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3"
2. Zlib zip library (package zlib1g-dev in ubuntu)
3. GSL development headers (package libgsl0-dev in ubuntu)

There are probably other requirements which are present on most systems by default.  If you encounter any problems let us know.  An up-to-date list of all requirements will be maintained on www.paintmychromosomes.com "Download" page.

2. INSTALLATION

Briefly:

./configure
make
make install #optional

More details are in the INSTALL file.

3. FURTHER INFORMATION

You need to prepare your data in CHROMOPAINTER format. This is nearly the same as PHASE format, but HAS BEEN UPDATED since chromopainter v 0.0.5.

Run "fs" for help. Examples are included in the "examples" directory; it is recommended to work through the examples to establish how to run this program on your own dataset.

IMPORTANT: If you have a small dataset, you can run 
"fs project -phasefile <data> -recombfile <recombination map file> -go"
and it will do everything with default settings that should work. BUT IF YOU HAVE A LARGE DATA SET THIS IS GOING TO TAKE A LONG LONG TIME. You will want to parallelise the work, which is done with the "-hpc" flag. You can then run commands on your own HPC or in parallel on a multi-core machine.

The examples show you how to do this!

www.paintmychromosomes.com is the place to start for help.  Visit the FAQ page for standard issues.
