Chorny, Ilya wrote:
> 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.

Hi Ilya,

What's your umask on the command line?  Galaxy tries to honor this umask
if possible, see the collect_associated files method of the Tool class
in lib/galaxy/tools/__init__.py.

--nate

> 
> Best,
> 
> Ilya
> 
> 
> Ilya Chorny Ph.D.
> Bioinformatics - Intern
> icho...@illumina.com<mailto:icho...@illumina.com>
> 858-202-4582
> 

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