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Installation Instructions for Ragout

Ragout is available for Mac OS and Linux.

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 [] or HAL Tools []

Binary Distribution

Pre-compiled binaries are available for Linux and Mac OS from 
the releases page [].
In this case you will not need the installation procedures below.


To build Ragout native modules, type:

You will also need either *Sibelia* or *HAL tools* installed (see below)


To build and install Sibelia, use:

        python scripts/

If you already have Sieblia installed into your system, it will
be picked up automatically by Ragout.

HAL Tools

HAL alignment produced by *Progressive Cactus* 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 []
as it is described in the manual. Do not forget to properly set PATH and PYTHONPATH
environment variables.


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

A: Probably your compiler is too old and does not support C++0x. Minimum required
versions of GCC and Clang are given in the beginning of this document.

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

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