On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
> We're currently looking at changing our Galaxy setup to link user accounts
> with Linux user accounts for better cluster integration (running jobs as the
> actual user on SGE). As part of this, we've tried setting up a fresh
> installation on a new VM which has thrown up some issues.
> [snip]

The next problem on my list was jobs successfully submitting to SGE
and running, then failing with a Python exception:


These emails from Donald Shrum and Jingchao Zhang (BCC'd) look
very similar, although I don't see they ever had a reply/resolution:


We eventually realised that the new Galaxy VM server was running
Python 2.7 (default under CentOS 7), but the cluster nodes were
running Python 2.6 (default under CentOS 6).

(Our current Galaxy server is also still running CentOS 6, which is
likely why I never hit this before.)

Replacing the VM with CentOS 6 we were able to get this to
work - but was that necessary? How exactly do the cluster jobs
invoke Python (especially when run as the associated Linux
user account rather than under the Galaxy Linux account)?

Sadly the cluster documentation does not mention Python at all:


This seems to be an oversight,


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