We had this topic at the GCC this year, especially within the Galaxy
Admins BoF. The truth is (please correct me anyone if this is not the case
anymore!) that you are touching an unresolved point. Keeping track of
tools, settings etc. across the versions is not given. People have their
'home-brew' solutions for this, e.g. keeping a (maybe virtual) machine in
spare in order to invest several hours up to some days to test (with or
without participation of the users) applicability to local
constraints/histories/workflow/tools. The more testing is automated and
the less users (or non-default pieces) the faster the update procedure can
be. But there are also instances which did not receive updates for months
or even years.
On our side we will be facing reality within the next two weeks as we
really need the update. Although preconditions are pretty good (few users,
not that deep modifications, high grade of automation) we expect some
issues. happy to have a virtualized environment...
To wrap up my answer in a nutshell: no, there is no best practice guide
and no migration tool, but every single contribution is warmly welcome :).
It would be *very* interesting how updates are handled at Galaxy Main...?
(very interested in further feedback)
> I try to keep our Galaxy instance up to date.
> Very often, some tools disappear and other do not work anymore. This
> breaks some users workflows.
> I may miss something. Is there a "best update pratice" to keep a Galaxy
> instance and the tool-sheds fully functionnal ?
> Thomas Bellembois, Network and System Administrator, IGFL (France)
> http://perso.ens-lyon.fr/thomas.bellembois - +33 4 26 73 13 67
> (IGFL internal IT doc: http://itdoc.igfl.ens-lyon.fr/itdoc)
> Please keep all replies on the list by using "reply all"
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Sebastian Schaaf, M.Sc. Bioinformatics
Faculty Coordinator NGS Infrastructure
Chair of Biometry and Bioinformatics
Department of Medical Informatics,
Biometry and Epidemiology (IBE)
University of Munich
Marchioninistr. 15, K U1 (postal)
Marchioninistr. 17, U 006 (office)
D-81377 Munich (Germany)
Tel: +49 89 2180-78178
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:
To search Galaxy mailing lists use the unified search at: