Some of these tools are or can be used on different operating systems, some are specific to a particular OS or class of OS (ex. Unix). The description of each tool will specify which platforms it runs on and how to install the tool for each of them. Different models use different tools sets. See the documentation for each model, accessible from models, for the tool set it needs. page.
Be sure to check if a tool is already installed before trying to install it again. This is often done by using the "--version" command line option for those tools that are programs that can be invoked from a terminal window command line. See the decription for a tool for more information on how to determine if the tool is installed.
There is a script for setting up a Ubuntu system with many of these tools. See the Kirschner Lab system administrator about setting up an Ubuntu system this way. It uses the following commands:
/usr/bin/apt-get -y install libqt4-dev
/usr/bin/apt-get -y install libboost-dev
/usr/bin/apt-get -y install subversion
/usr/bin/apt-get -y install eclipse
/usr/bin/apt-get -y install mencoder
/usr/bin/apt-get -y install vlc
/usr/bin/apt-get -y install gnuplot
/usr/bin/apt-get -y install qt-dev-tools
/usr/bin/apt-get -y install texlive-latex-base
/usr/bin/apt-get -y install texlive-latex-extra
/usr/bin/apt-get -y install texlive-latex-recommended
/usr/bin/apt-get -y install libboost-program-options-dev
/usr/bin/apt-get -y install mesa-utils
/usr/bin/apt-get -y install g++
/usr/bin/apt-get -y qtcreator
On Ubuntu systems always perform sudo apt-get update before performing
any other apt-get commands. This ensures that the system knows the latest information
about the packages that can be installed - the current locations of the current versions.
Otherwise it is possible not all necessary files are installed and model builds may fail.