> This script is used multiple times, so you might want to make sure that this 
> change won't cause files to become readable that you would prefer remain 
> unreadable.

>From the log output, it looks like files are chmod'd to the user, then later 
>back to the Galaxy user.  Is there somewhere else that isn't logged?

> Since you mention Apache uploading, what are you using for Apache to handle 
> the uploads?

I don't know, whatever the default mechanism.  I'm not using nginx.

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