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General Notes

All software is published under the MIT license.

All software published here is designed for the Linux operating system. Although some pieces are platform-independent (e.g., R packages), and other pieces can be run under Windows operating system in Cygwin environment, we never provide specific instructions for environments other than Linux OS.

All of our software was tested under CentOS 7.

Use the menu on the left side of this page to navigate between various topics. Top-level items in the menu usually serve as titles for topics below them. However, these items correspond to separate pages that could contain useful information. Please be sure to visit top-level pages — otherwise, you could miss important information.

Conventions used in software installation documentation

All commands in the code snippets and all other instructions are given with the assumption that you install software in   $HOME/Software   directory. If you prefer another location, or if you install software in the way that it is available for other users, please make changes accordingly.

When a code snippet has a web-link to a downloadable file, it may link to an older version. Always consult the Downloads page to get the most recent version, and update the code snippet accordingly.

Conventions used in code blocks

In code blocks that demonstrate interaction in terminal, the command that you have to type are typeset in blue, and what computer responds is in black.

In the terminal, your command usually is preceded with shell prompt. We never show this prompt in code blocks, in order to simplify cut-and-paste code from website to the terminal.

Recommended way to add a path to $PATH permanently

We recommend that you use .bashrc to make permanent addition to PATH environmental variable. Add the following code to the end of your .bashrc file (replace the example path by the one that you need):

if [[ ! "$PATH" =~ "$path_addition" ]]; then
    export PATH="$path_addition:$PATH"

After updating .bashrc either log out and log in again, or execute the following command:

source .bashrc