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Requirements


BIRCH currently has the following dependencies:
    1. Java Runtime Environment, version 8 or newer
    2. Python 2.7  AND Python 3
    3. Csh/Tcsh installed
You can check if you have these by running this script, or by typing these commands at a terminal:
Java:
java -version should output 1.8 or greater Important: If the word "headless" appears, you must install the full Java JDK.

Python:
python --version

python3 --version
should output 2.7 or greater

should output 3.6 or greater

 Tcsh/csh
tcsh --version


if it outputs anything it should be good enough...


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
    >>>


A more comprehensive list of dependencies can be found at Dependencies.

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

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. Check whether java is headless:
    dpkg -l |grep openjdk
    If you have the headless version of Java, uninstall it:
    sudo apt-get remove openjdk-8-jre-headless
  3. Execute:
sudo apt install default-jdk
sudo apt-get install python numpy python3
sudo apt-get install tcsh

For Ubuntu 22:

sudo apt-get install python-is-python3

With Ubuntu 22, there is no 'python' command. This package creates an alias so that 'python' will run 'python3'. Since many of the Python calls in BIRCH are just to 'python', many of the scripts won't work unless you install this package.

Fedora
  Fedora/RedHat
CentOs

  1. Open a terminal
  2. Execute:
    1. su #become administrator
    2. yum install java python tcsh
    3. yum install numpy
Fedora31 (and possibly other RedHat-derived linux distros) have ONLY the headless Java installed by default. Before running getbirch.jar, you need to install the full JKD using the following command:

sudo dnf install java-latest-openjdk.x86_64
Linux
(Other Linux distros)
  1. Download and install Java
  2. Download and install Python
  3. Download and install tcsh
  4. Download and install numpy