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 Requirements


BIRCH currently has the following dependencies:
    1. Java Runtime Environment, version 8 or newer
    2. Python 3
    3. Csh/Tcsh installed
    4. MacOS - also requires Xcode, which is available at the App Store.
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:
python3 --version 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}python3
    Python 3.6.8 (default, Oct  2 2023, 21:12:58)
    [GCC 8.5.0 20210514 (Red Hat 8.5.0-18)] on linux
    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
    Shortcut: If you type 'python3 --version', you will be prompted to install python, which in turn will install Xcode as a dependency. Thus, both python3 and Xcode are installed in a single step.
  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 numpy python3
sudo apt-get install tcsh
Fedora
  Fedora/RedHat
CentOs
  1. Open a terminal
  2. Execute:
    1. su #become administrator
    2. yum install java 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