Complete Genomics Analysis Tools 1.3.0 Readme For full documentation on cgatools, see http://cgatools.sourceforge.net/. Dependencies To build cgatools from source, the following dependencies must be installed first: * cmake >= 2.8 * boost = 1.42 * python >= 2.4.3 (only if running test cases) * doxygen >= 1.6.2 (only if generating API docs) Installation For detailed install instructions, see cgatools-install.pdf, included in the cgatools release. Quick Start Install from Source Cgatools uses the cmake build system. Only out-of-source builds are supported. So on a UNIX-like system, from an empty directory, the following will build and install cgatools: cmake -DBOOST_ROOT=/path/to/boost/root \ -DCMAKE_INSTALL_PREFIX=/path/to/install/dir \ -DCMAKE_BUILD_TYPE=Release \ /path/to/source/dir make -j8 && ctest -j8 && make -j8 install Note that the /path/to/boost/root is the same as the path you gave as the --prefix option when installing boost. After installation, you should be able to run /path/to/install/dir/bin/cgatools for further help. Tips for Installing Dependencies Cmake may not be able to find boost if cmake's processor architecture differs from boost's. For example, if you have a 64-bit version of boost installed, you must have the 64-bit version of cmake. If installing dependencies from source, remember to set the install prefix, as described by the documentation for the dependency you are installing. Tested Environments Cgatools was tested on these platforms: * GCC 4.1.1 on CentOS with cmake 2.8, boost 1.42, python 2.4.3. * GCC 4.2.1 on Mac OS X with cmake 2.8.2, boost 1.42, python 2.6.1. Changelog For a list of changes, see cgatools-release-notes.pdf, included in the cgatools release.