Found a fix. The external_chown_script.py script forcibly changes the permissions on the file to be world-readable.
diff external_chown_script.py external_chown_script.py.ORIG 33d32 < os.system('chmod -R a+r %s' %(path))
Please let me know if this is a bad change or if there is a better change.
David
Begin forwarded message:
From: David Hoover hooverdm@helix.nih.gov Date: October 2, 2012 1:21:02 PM EDT To: Oleksandr Moskalenko om@hpc.ufl.edu Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] submitting jobs as the real user
No, that's not it. The galaxy user, as well as all other users, have umask 022 by default.
I believe the problem is with Apache uploading. I can't figure out how to reconfigure Apache to set the permissions they way I want them.
David
On Oct 2, 2012, at 1:17 PM, Oleksandr Moskalenko wrote:
Hi David,
I wonder if the user's umask is the problem.
I set the galaxy user's umask to 022 and our default umask on the cluster is 0022 for all users.
On Oct 2, 2012, at 12:55 PM, David Hoover hooverdm@helix.nih.gov wrote:
I'm playing with the "submitting jobs as the real user" method, and immediately ran into a problem. Uploaded files are created in mode 600, owned by the user. Galaxy then gives an error that the tmp file is not readable:
IOError: [Errno 13] Permission denied: '/spin1/users/galaxy/galaxy2/database/tmp/tmp3KHIDt'
Is there any way of changing the permissions on the temporary uploaded file to 666?
David Hoover Helix Systems Staff ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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