Peter - Nate and I are in agreement that the goal is to eliminate that directory, so I don't want to put effort into automating its creation.
https://github.com/galaxyproject/galaxy/issues/1576 If you wish to open a PR that does this though, I would be happy to merge this. The best place to ensure this directory exists is in the drmaa runner where it is being used. -John On Mon, Jan 25, 2016 at 4:20 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > 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 > ___________________________________________________________ > 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/ ___________________________________________________________ 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/