There is certainly no flag in Galaxy to allow this. Even if you tried to hack it in - there would be some problems. Galaxy writes out some files to that working directory before running the job - so there would need to be more chown-ing and stuff happening at the beginning of the job - probably before it even got to the runner component. If Galaxy could assume these directories already existed and didn't need to run the jobs as the real user - this would be a lot easier (not easy, just easier) to hack into Galaxy - but I assume you want to run these jobs as the real user. I've created a Trello card for this request: https://trello.com/c/n1UitJTb. Sorry I don't have better news. -John On Wed, Jun 25, 2014 at 3:51 PM, Shrum, Donald C <DCShrum@admin.fsu.edu> wrote:

I'd like to set the job_working_directory to the user's home directory.

I'm using an apache proxy with ldap authentication. I'm assuming I need to strip the remote_user_maildomain off the user name to do something like...

job_working_directory = ~%user/galaxy_working_directory

Is this possible?

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