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.

First of all, what is the status of the old set_metadata_externally setting? This is described on the legacy documentation page as required under "Submitting Jobs as the Real User",

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster/Legacy

Unfortunately, the same text is still present on the current page:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster/

According to the GitHub search, set_metadata_externally no longer exists in the code or default settings files:

https://github.com/galaxyproject/galaxy/search?q=set_metadata_externally

I eventually tracked this down to the following commit, first included in Galaxy v13.06, back when the config file was universe_wsgi.ini rather than config/galaxy.ini,

https://github.com/galaxyproject/galaxy/commit/68065e123800a5a2e700d636db935...

So, can we assume that metadata is now always set externally, and should the wiki be updated accordingly?

Thanks,

Peter

I've gone ahead and removed the references to set_metadata_externally from https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster/ but the text also covered outputs_to_working_directory as well: """ The set_metadata_externally and outputs_to_working_directory options in the Galaxy config must be set to True. set_metadata_externally is always recommended for Galaxy servers running outside of a single user's development environment. outputs_to_working_directory ensures that a tool/job's outputs are written to the temporary working directory, which (when using the real user system) is owned by the real user who submitted the job. If left set to the default (False), the tool will attempt to write directly to the directory specified in file_path (by default, galaxy-dist/database/files/), which must be owned by the Galaxy user (and thus will not be writable by the real user). """ Does the new version make sense?: """ The outputs_to_working_directory option in the Galaxy config must be set to True. This ensures that a tool/job's outputs are written to the temporary working directory, which (when using the real user system) is owned by the real user who submitted the job. If left set to the default (False), the tool will attempt to write directly to the directory specified in file_path (by default, galaxy-dist/database/files/), which must be owned by the Galaxy user (and thus will not be writable by the real user). """ Diff: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?action=diff&rev1=53&rev2=54 Peter