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INSTALL Guide For MACS

Time-stamp: <2014-06-17 15:27:24 Tao Liu>

Please check the following instructions to complete your installation.

Prerequisites

Python version must be equal to 2.7 to run MACS. I recommend using the version 2.7.2.

Numpy (>=1.6) are required to run MACS v2.

GCC is required to compile .c codes in MACS v2 package, and python header files are needed. If you are using Mac OSX, I recommend you install Xcode; if you are using Linux, you need to make sure python-dev is installed.

Cython (>=0.18) is required only if you want to regenerate .c files from .pyx files using setup_w_cython.py script.

Easy installation through PyPI

The easiest way to install MACS2 is through PyPI system. Get pip if it's not available in your system. Note if you have already installed numpy and scipy system-wide, you can use `virtualenv --system-site-packages` to let your virtual Python environment have access to system-wide numpy and scipy libraries so that you don't need to install them again.

Then under command line, type `pip install MACS2`. PyPI will install Numpy and Scipy automatically if they are absent.

To upgrade MACS2, type `pip install -U MACS2`. It will check currently installed MACS2, compare the version with the one on PyPI repository, download and install newer version while necessary.

Note, if you do not want pip to fix dependencies. For example, you already have a workable Scipy and Numpy, and when 'pip install -U MACS2', pip downloads newest Scipy and Numpy but unable to compile and install them. This will fail the whole installation. You can pass '--no-deps' option to pip and let it skip all dependencies. Type `pip install -U --no-deps MACS2`.

Install from source

MACS uses Python's distutils tools for source installations. To install a source distribution of MACS, unpack the distribution tarball and open up a command terminal. Go to the directory where you unpacked MACS, and simply run the install script:

$ python setup.py install

By default, the script will install python library and executable codes globally, which means you need to be root or administrator of the machine so as to complete the installation. Please contact the administrator of that machine if you want their help. If you need to provide a nonstandard install prefix, or any other nonstandard options, you can provide many command line options to the install script. Use the –help option to see a brief list of available options:

$ python setup.py --help

For example, if I want to install everything under my own HOME directory, use this command:

$ python setup.py install --prefix /home/taoliu/

If you want to re-generate .c files from .pyx files, you need to install Cython first, then use setup_w_cython.py script to replace setup.py script in the previous commands, such as:

$ python setup_w_cython.py install

or:

$ python setup_w_cython.py install --prefix /home/taoliu/

Configure enviroment variables

After running the setup script, you might need to add the install location to your PYTHONPATH and PATH environment variables. The process for doing this varies on each platform, but the general concept is the same across platforms.

PYTHONPATH

To set up your PYTHONPATH environment variable, you'll need to add the value PREFIX/lib/pythonX.Y/site-packages to your existing PYTHONPATH. In this value, X.Y stands for the major–minor version of Python you are using (such as 2.7 ; you can find this with sys.version[:3] from a Python command line). PREFIX is the install prefix where you installed MACS. If you did not specify a prefix on the command line, MACS will be installed using Python's sys.prefix value.

On Linux, using bash, I include the new value in my PYTHONPATH by adding this line to my ~/.bashrc:

$ export PYTHONPATH=/home/taoliu/lib/python2.7/site-packages:$PYTHONPATH

Using Windows, you need to open up the system properties dialog, and locate the tab labeled Environment. Add your value to the PYTHONPATH variable, or create a new PYTHONPATH variable if there isn't one already.

PATH

Just like your PYTHONPATH, you'll also need to add a new value to your PATH environment variable so that you can use the MACS command line directly. Unlike the PYTHONPATH value, however, this time you'll need to add PREFIX/bin to your PATH environment variable. The process for updating this is the same as described above for the PYTHONPATH variable:

$ export PATH=/home/taoliu/bin:$PATH

-- Tao Liu <vladimir.liu@gmail.com>