I'm CC'ing the Galaxy-Dev list on my response to your question.
I talked with Jen Jackson on this. Her suggestion is that the symlink is
most likely the problem somehow - this time. When in doubt, getting rid of
these good place to start. So recommended starting solution to try - use
full paths for everything. Also probably keep all on same partition for
the best performance, but that would be hard to defend (there was some
debate about this recently).
Many thanks to Jen for her (as always) careful consideration.
On Mon, Nov 5, 2012 at 7:15 AM, Alan V. Cowles <alan.cow...@duke.edu> wrote:
> Hey Dave,
> Thanks for getting back in touch with me.
> We are running our galaxy instance on a vm... with Centos (RHEL) 6.2, 2
> vcpus, and 2gb vram, with a remote postgresql prod server as our database
> Our first issue was trying to get it so we could load sequence and larger
> files directly from an nfs mounted directory on the server, without
> uploading via the web (php vs large files problem.) We accomplished this
> via the data libraries interface but it's still not very user intuitive.
> Our first demo user attempted to upload 3 large files and actually filled
> up the / partition on the server as galaxy was installed at /usr/local.
> After scrapping and rebuilding that, we now have a several hundred GB nfs
> partition, mounted and /usr/local/galaxy is a symlink to a folder on this
> The issue we are currently seeing is during an upload, or even just
> linking files it runs for a while before erroring out and saying there is
> no information on the error. The file seems to be there and taking up the
> correct amount of disk space but galaxy has a red bar.
> The galaxy server instance is running back grounded in a screen so we can
> always switch over and look at the output it shows to standard out as
> errors happen, and it seems that it has trouble changing permissions on the
> files in the nfs directory, even though, root squash is disabled, and the
> entire directory is 777 at the top level and everything underneath is owned
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