On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <[email protected]> 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 ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
