When I run galaxy as the actual user using the code I committed to my fork, I 
run into a problem with dataset_*.dat files that have associated data wherein 
the associated data files are copied from the job_working_directory into the 
files directory. That directory is owned by the actual user and not by the 
galaxy user. I don't have a problem with the ownership but the permissions of 
the directory and associated files get changed to 777. Any thoughts on why the 
permissions get changed. The permissions are 755 and 644 for dirs and files 
respectively when in the working directory so why do they change when the 
directory is moved?

Any help would be greatly appreciated.



Ilya Chorny Ph.D.
Bioinformatics - Intern

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