Thanks to the helpfull message of John, I am now able to backup and retrieve my users from a galaxy to another without using directly the database (by using the galaxy model and sql alchemy).

I am trying to do the same thing for workflows, libraries, datasets and histories.

The repository is here:

Any interest/participation is welcome.

Best Regards

2014-11-21 17:50 GMT+01:00 John Chilton <jmchilton@gmail.com>:
This is a tough question - I suspect it will be difficult no matter
how you proceed. The API objects don't map 100% directly to database
objects and may not have complete coverage - but using the database
directly will require one to learn a lot of Galaxy's data model I

A middle ground - would be to just use the Galaxy code and ORM layer
without running a Galaxy server (see scripts/db_shell.py for

My gut tells me it is probably be easiest (least difficult anyway) to
target the database directly - but this could be wrong.


On Wed, Nov 19, 2014 at 6:21 AM, Rémy Dernat <remy.d1@gmail.com> wrote:
> Hi,
> I would like to create a code to backup and migrate(*) galaxy datas, based
> on the api and/or with the script I did here:
> https://github.com/remyd1/galaxy_debug_params/blob/master/source/Templates/parameters/generate_shell_script.mako
> To do that, I would use the galaxy model, to retrieve everything in the old
> one and recreate everything in the new one.
> However, I would like to be able to do that without my web server running.
> That is to say, a "cold" migration to avoid any current task to write
> additionnal things into the database. Obviously, that is a problem for the
> api because this one use the web server.
> Could you give some advice to do that ? Should I recreate a code from 0 ?
> Could I use the code in the api ? Is there a way to create a code that could
> use the api differently (recreate a copy of the api without the web server)
> ?
> Kind regards,
> Remy
> (*) this is important; that means you could import data from an old galaxy
> to a recent one (or the opposite); a simple backup of files and a dump of
> the db is not enough.
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