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Requirements


BIRCH currently has the following dependencies:
    1. Java Runtime Environment, version 6 or newer (8 is preferred!)
    2. Python 2.6 or newer (newer preferred!) Warning: BIRCH is not yet Python 3 compliant.
    3. Csh/Tcsh installed
You can check if you have these by running this script, or by typing these commands at a terminal:
  1. Java:
    1. java -version #should output 1.6 or greater
    2. which java  # should output a path like /usr/bin/java
  2. Python:
    1. python --version # should output 2.6 or greater
    2. which python #should output a path like /usr/bin/python
  3. Tcsh/csh
    1. tcsh --version #if it outputs anything it should be good enough...
    2. which tcsh #should output a path like /usr/bin/tcsh
Optional dependencies - BIRCH will function without these, but specific programs require them.
  • numpy - Python numerical libraries, required by WebLogo. If numpy is installed you should be able to run python and try to import numpy. (User input shown in bold below). If you get an error, you need to install numpy.
    {venus:/home/psgendb}python
    Python 2.6.6 (r266:84292, Nov 21 2013, 10:50:32)
    [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
    Type "help", "copyright", "credits" or "license" for more information.
    >>> import numpy
    >>>


If you are missing one of them, follow the steps below:

Solaris
  1. Download and install Java
  2. Download and install Python
  3. Download and install numpy
Mac OS X
  1. Update to the newest version of java using the update manager
  2. Download and install Python
  3. Download and install numpy
Ubuntu
Ubuntu/Debian
  1. Open a terminal
  2. Execute:
    1. sudo apt-get install java python tcsh
    2. sudo apt-get install python-numpy
Fedora
  Fedora/RedHat
CentOs

  1. Open a terminal
  2. Execute:
    1. su #become administrator
    2. yum install java python tcsh
    3. yum install numpy
Linux
(Other Linux distros)
  1. Download and install Java
  2. Download and install Python
  3. Download and install tcsh
  4. Download and install numpy
Windows
Windows XP,Vista,7

Under development
BIRCH is not yet available on Windows, but we're getting there.

Our plan is that you should only need:
  1. Java installed
  2. Administrative privileges (hopefully not!)