System Environment Setup

Biomolecule Toolkit requires an application home directory, which will be identified by an environment variable called BIOREG_HOME. This application home directory must have read and write access rights for the user context that runs the container application (e.g. Tomcat) and must contain the bioreg.properties file. It is also required to set a JAVA_HOME environment variable pointing to an appropriate Java JDK or JRE installation.

Creating environment variables


Example 1 for Windows

Run Command Prompt as an administrator and enter:

 setx -M BIOREG_HOME "C:\path\to\any\directory"

Verify that the environment variable is set up correctly by using echo %BIOREG_HOME% in the command prompt. you should see the path which you defined above as output.

Example 2 for Windows

In Control Panel, open Edit the system environment variables menu, then click on System variables button. Here, you can create new system variables by adding the corresponding folder location.

In the above mentioned menu, you can set the JAVA_HOME environment variable if needed. In this case, add the jdk or jre folder location (e. g. C:\Program Files\Java\jdk1.8.0_191) before you proceed with the installation.

Example for Linux

The following examples represent a convenient method for using and storing command lines in bash profile. To do so, run terminal and start by opening .bash_profile within e.g. the nano text editor:

 nano ~/.bash_profile

Add the following line to the .bash_profile

export BIOREG_HOME=/Users/<USERNAME>/.chemaxon/bioreg/ 

Save the changes made to .bash_profile and exit nano.

Example for MacOS

In terminal, start by opening .bash_profile within the nano text editor:

 nano ~/.bash_profile

Then set the environmental variable:

export BIOREG_HOME=$(/usr/libexec/java_home) 

Save the changes made to .bash_profile and exit nano.

If Tomcat was running while you created or edited the environment variable, a restart of Tomcat is required.