INSTALL

INSTALL Guide For AREM
Time-stamp: <2011-03-01 18:21:42 Jake Biesinger>

Please check the following instructions to complete your installation.

* Prerequisites

Python version must be equal to 2.6 or 2.7 to run AREM. We recommend
using the version 2.6.5.

* INSTALLATION

** Install using easy_install or pip

If you have python's easy_install program (http://pypi.python.org/pypi/setuptools)
or the pip program (http://pypi.python.org/pypi/pip), then installing AREM is just
one command away:

$ easy_install AREM
-OR-
$ pip install AREM

You can also request a particular release of AREM (for example, version 1.0.1) using:

$ pip install AREM==1.0.1


** Install under Debian or Ubuntu Linux system

The most convenient way to install AREM is through Debian APT system,
so that it can be perfectly integrated in the Python environment of
your operation system. You can easily manage the package, and the
uninstall is much easier. Download the deb package from MACS download
page, and type this in the commend line:

$ dpkg -i macs_1.4.0rc2.deb

To uninstall, type:

$ dpkg -r macs_1.4.0rc2

This is tested only in Ubuntu 10.10 and 10.04 LTS.


** Install from source

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


* 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 2.6 or 2.7 ; you can find this with
sys.version[:3] from a Python command line). PREFIX is the install
prefix where you installed AREM. If you did not specify a prefix on
the command line, AREM 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/python2.6/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 AREM 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

* About PeakSplitter

Please go to it's main site
<http://www.ebi.ac.uk/bertone/software.html> to download.

* About GSL package

From MACS version 1.2, I have removed GSL -- GNU Scientific Library,
from the distribution.

--
Tao Liu <taoliu@jimmy.harvard.edu>
Jake Biesinger <jake.biesinger@gmail.com>