Complete Genomics Analysis Tools 1.0.0 Readme


Dependencies

To build cgatools from source, the following dependencies must be
installed first:

* cmake >= 2.8
* boost >= 1.35 (1.42 recommended)
* 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.


Changelog

* 1.0.0.15 (patch)
  * fixed snpdiff and calldiff failure processing male build 37 genomes
* 1.0.0.14 (patch)
  * fixed evidence2sam for genomes with format version 1.0
* 1.0.0.13 (patch)
  * changed to dynamic linkage on Mac OSX
* 1.0.0
  * cgi2sam renamed map2sam
  * evidence2sam (beta)
* 0.5.0 (Initial version)
  * reference tools
  * snpdiff
  * calldiff
  * cgi2sam