Re: [galaxy-dev] Removing set_metadata_externally from wiki documentation?

[Rémy Dernat]

Hi Peter,

I am also quite interesting with these settings. If you achieve this
configuration please keep us inform.

Best
Remy
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Re: [galaxy-dev] Removing set_metadata_externally from wiki documentation?

[Peter Cock]

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock  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/68065e123800a5a2e700d636db9354702ac42fe5
>
> 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=53=54

Peter
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[galaxy-dev] Removing set_metadata_externally from wiki documentation?

[Peter Cock]

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/68065e123800a5a2e700d636db9354702ac42fe5

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

Thanks,

Peter
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