Installation Instructions for Ragout
====================================

Availability
------------
Ragout was tested under Mac OS and Linux. While it should work
under Windows, we currently do not provide an official support.


Build Requirements
------------------
* C++ compiler with C++0x support (GCC 4.6+ / Clang 3.2+ / Apple Clang 4.2+)
* GNU make / Cmake (for building Sibelia)


Runtime Depenencies
-------------------

* Python 2.7
* Sibelia [http://github.com/bioinf/Sibelia] or HAL Tools [https://github.com/glennhickey/hal]


Binary Distribution
-------------------

Pre-compiled binaries are available for Linux and Mac OS from 
Releases page: https://github.com/fenderglass/Ragout/releases
In this case you will not need any installation procedures.


Building
--------

1. To build Ragout native modules, type:
    
        make

2. To build and install Sibelia, use:

        python scripts/install-sibelia.py

If you already have Sibelia installed or do not need it, 
you can skip the second step.


HAL Tools
---------

HAL alignment could be used for synteny blocks decomposition instead of Sibelia
(recommended for large genomes). If you want to use HAL alignment as input,
you need to install HAL Tools package: https://github.com/glennhickey/hal.
Follow the manuals and do not forget to properly set PATH and PYTHONPATH
environment variables as it is described.


Troubleshooting
---------------

Q: Different errors during compilation, possibly with 
"unrecognized command line option '-std=c++0x'" message:

A: Probably your compiler is too old and does not support C++0x. Minimum
versions of GCC and Clang are mentioned at the beginnig of this documtent.


Q: "libstdc++.so.6: version `CXXABI_1.3.5' not found" or similar error when running

A: Ensure that the version of libc++ used to compile Ragout is similar
to one the you currently trying to use. You can specify an extra search path
to a specific library by setting "LD_LIBRARY_PATH" variable.