I installed the latest Galaxy (v15.07) and tested with a job. I found my local environment setup file was not executed. The line of code that executes the local setup file is [ -f "config/local_env.sh" ] && . config/local_env.sh Further looking into the galaxy_xx.sh file shows the current directory of the script is $working_directory before "cd $working_directory" is executed. This is not the case in previous versions, where the job's current directory is the root of the Galaxy server in the beginning, until "cd $working_directory" is executed. I think making the current directory first at the root of the Galaxy server is better since I don't need to put a full path in galaxy.ini for the environment_setup_file. Will you change this back to it was? Thanks, Ping