So we have forked the stable branch of galaxy and are making our own modifications. We are running galaxy on Ubuntu 14.04.1 LTS and we're using modules to load the underlying software, i.e. set environment variables. This works just fine for PATH, JAVA_JAR_PATH, PYTHONPATH, etc., however, LD_LIBRARY_PATH is not being passed to the tools. When a tool (such as cuffdiff) tries to access LD_LIBRARY_PATH, it is empty. We've checked to make sure that loading the cufflinks module correctly updates the LD_LIBRARY_PATH, however, when it is used in galaxy, all the other environment variables are set properly, but not LD_LIBRARY_PATH. Does anyone have any ideas on why this would happen and how to fix it?