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]

We eventually got Galaxy to talk to SGE and submit jobs successfully
as the individual user's Linux account, with external_chown_script.py
being called to handle ownership of the files.

One small stumbling block was missing the cluster_files_directory directory.
https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample
says:

# If using a cluster, Galaxy will write job scripts and stdout/stderr to this
# directory.
#cluster_files_directory = database/pbs

According the the current code, this is still the default value being used:

https://github.com/galaxyproject/galaxy/blob/274af50792aaaf367520c22d7c13e22e70000d4d/lib/galaxy/config.py#L170

However, Galaxy itself did not seem to create the cluster_files_directory
directory - and there doesn't seem to be a ready-made pbs folder in the
git repository. Should that happen automatically?

At one stage, run.sh would create database/files and database/tmp -
I'm note sure what that happens now:

https://github.com/galaxyproject/galaxy/commit/4d720d63c631862778e54bd68c4e375438ba3ea5
https://github.com/galaxyproject/galaxy/commit/7560751dc87492471880c82b00857af12565c06b

Peter
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