On 06/12/2012 04:04 PM, Joachim Jacob wrote:
Hi Hans-Rudolf,

Thank you for sharing your experience!

To summarize:
1. user information is stored in the database (histories, pages,
workflows). This info is linked to the datasets,
2. all datasets are in the '../database/files' (or the location
specified in universe_wsgi.ini) directory, and
3. all configuration files are located in the root of Galaxy.

So would it be feasible to run the postgresdb not locally, but on a
separate machine, to which I connect the freshly installed Galaxy?
Then I can also keep the datasets directory on a network share, which is
mounted to the fresh install.
[perhaps other directories can also be accessed over the network, such
as the toolshed tools directory].

No, don't share the postgresdb and the datasets. Two different galaxy installations accessing the same postgresdb and the datasets will cause troubles.

Hence, I have step 6 and 7 in my procedure, to make sure all the data accumulated during the test phase gets 'replaced' with all the data the users continue to produce on the old production server.

The configuration files is perhaps the most difficult part. these have
to be merged. But perhaps I could use mercurial for this? Seems a
powerful way to do this.

Yes, to some extend, see the ".hgignore" file

Regards, Hans


Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)

On 06/12/2012 02:29 PM, Hans-Rudolf Hotz wrote:
Hi Joachim

This is roughly what we did ~15 months ago:

1. make a copy of the MySQL DB (postgresdb in your case)

2. copy the complete galaxy directory to the new server (make sure you
keep the path)

3. point the new galaxy server to the DB copy and start it (different
port number)
-> due to the higher Python version, news eggs were downloaded
-> all python code was re-compiled

4. test the new server (while the old one is still in use)

5. stop the old server

6. rsync ~/galaxy_dist/database/files/

7. point the new galaxy server to the 'live' DB and re-start it

Obviously, this is won't be a 'fresh' Galaxy install.

If you want to start from a new download of the galaxy distribution,
the amount of work (eg: merging of configuration files) depends on the
existing modifications you have made. If you have only a few, the
copy/merge of the: universe_wsgi.ini and tool_conf.xml files
plus a copy of the database/ and tools/ directory might be
sufficient...or you need to look into the tool-data/ directory, the
datatypes_conf.xml file, etc, etc....but you can test all this while
the new server is already running in parallel to the current server.

Regards, Hans

On 06/12/2012 01:14 PM, Joachim Jacob wrote:
Hi all,

I am looking for instructions to migrate users, configuration and data
to other Galaxy machine. I have a production Galaxy, with users,
histories, pages, data libraries, configured tool panel, running on a
postgresdb. I want to move this information to a fresh Galaxy install
(same version as production) on another machine.

Is this feasible to do without much hassle? I am thinking about a
merge/sync of configuration files and dumping and creating the
postgresdb,... Has anyone experience with this and a check list for

The idea is that the user should have no clue that Galaxy is on a new
machine: all data, tools, histories, etc... are there. Thanks for your

Kind regards,

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