Installation

Required software for building MASon:
build-essentials (gcc, …)
cmake
zlib (Ubuntu: zlib1g-dev)
AMD-APP SDK (required for mapping on the CPU or on ATI GPUs)
cudatoolkit (required for mapping on Nvidia GPUs)

Build NGM:

wget https://github.com/Cibiv/NextGenMap/tarball/master -O NGM.tar.gz
tar xvfz NGM.tar.gz
cd Cibiv-NextGenMap*
mkdir -p build/release
cd build/release/
cmake -DCMAKE_BUILD_TYPE=Release ../..
make

cd ../../bin
./NGM

For BAM support Bamtools (http://sourceforge.net/projects/bamtools/) is required.
If the bamtools or the OpenCL includes/libs are not installed in the default directories (e.g. /user/lib) please add:

-DCMAKE_PREFIX_PATH="<path to bamtools folder>[;<path to opencl>]"

to the camke command.

Example:

cmake ../../ -DCMAKE_PREFIX_PATH="/software/ngm/src/bamtools/;/home/CIBIV/philipp_/AMD-APP-SDK/" -DCMAKE_BUILD_TYPE=Release

NGM was tested on openSUSE 11.4 (x86_64) with GCC 4.3.4. and on Ubuntu 12.04 (x86_64) with GCC 4.6.3