I am trying to create an environment variable of which will be stored in env.sh for an environment variable that already exists.
Essentially I am fetching predefined JAVA environment variables using the following:
R CMD javareconf -e
This command defines a series of environment variables, some of which include JAVA and JAVAC, etc.
I then try to do the following:
<environment_variable name="JAVA" action="set_to">$JAVA</environment_variable> <environment_variable name="JAVAC" action="set_to">$JAVAC</environment_variable>
But this does not store the value of $JAVA but instead "$JAVA".
Any suggestions on how to do this in galaxy without having to create a second env.sh?