BreakDancer uses CMake which is a cross-platform build tool. Basically it will generate a Makefile so you can use make. The requirements are the zlib, development library, gcc, gmake, cmake 2.8+. Beginning with version 1.4.4, BreakDancer includes samtools as part of the build process.

Here are the steps to build:

# --recursive option is important so that it gets the submodules too
$ git clone --recursive https://github.com/genome/breakdancer.git
Resolving deltas: 100% (38/38), done.
Submodule path 'build-common': checked out '...'

$ cd breakdancer
$ mkdir build
$ cd build

$ cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
-- Build files have been written to: .../breakdancer/build

$ make
Linking CXX executable ../../../../bin/breakdancer-max
[100%] Built target breakdancer-max

$ sudo make install