Complete Genomics Analysis Tools 1.4.0 README

For full documentation on cgatools, see http://cgatools.sourceforge.net/.


Installation

For detailed install instructions, see cgatools-install.pdf, included in the
cgatools release.


Quick Start Install from Binary

1. Untar the tarball

Linux
B2$ tar xzf cgatools-X.X.X.X-linux-x86_64.tar.gz

Mac OS X:
B2$ tar xzf cgatools-X.X.X.X-darwin-x86_64.tar.gz

2. Copy the executable and documentation into your binary directory:

Linux:  
B3$ cp cgatools-X.X.X.X-linux-x86_64/bin/cgatools /home/cgi/local/bin

Mac OS X:
B3$ cp cgatools-X.X.X.X-darwin-x86_64/bin/cgatools /home/cgi/local/bin

3. Be sure that the directory containing the cgatools executable (here,
/home/cgi/local/bin) is in your $PATH. Consult your shell documentation for
how to set the $PATH in your .tcshrc or .bashrc or paths file.


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)


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.


License

Copyright 2011 Complete Genomics, Inc.

   Licensed under the Apache License, Version 2.0 (the "License"); 
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.