On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock p.j.a.cock@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/274af50792aaaf367520c22d7c13e22...
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/4d720d63c631862778e54bd68c4e3... https://github.com/galaxyproject/galaxy/commit/7560751dc87492471880c82b00857...
Peter