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?
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