Question: old version galaxy update
0
gravatar for janecao999
5 months ago by
janecao9990
janecao9990 wrote:

Dear Galaxy developers, We have used an old version galaxy (May, 2012 release) in a local server for many years. The galaxy runs well with a few tools we routinely used. Due to security issues recently reported, we would like to update the galaxy to its current release. Could you suggest what is the best approach for us to update the galaxy or is it still possible to perform update from that old version of galaxy? If we have to make a new installation of galaxy, can we keep and migrate the data created from old version?

Thanks a lot for your help!

Jane

galaxy • 194 views
ADD COMMENTlink modified 5 months ago by Hotz, Hans-Rudolf1.8k • written 5 months ago by janecao9990
1
gravatar for Hotz, Hans-Rudolf
5 months ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

Hi Jane

In theory, an update should be possible despite the fact that Galaxy has changed from mercurial to git in 2015. Have a look at:

https://galaxyproject.org/develop/source-code/#How_to_migrate_a_Galaxy_instance_from_Mercurial_Bitbucket_to_Git_GitHub

Once you have changed, you can then do the actual update.

Depending on how many and what kind of local changes you've done in the Galaxy code, you might wanna consider a different approach:

  • install a fresh, up-to-date Galaxy server
  • point this new server to a copy of your (PostgreSQL) database, and run 'manage_db.sh upgrade'
  • copy the 'database' directory (i.e. all the datasets) from your existing server to the new server
  • add your local changes, like '.loc' files, '~/tool-data/shared/ucsc/chrom/.len' files, etc
  • add your local changes to 'galaxy.ini' (this is the replacement of the 'universwgs.ini' file), like add the admin users, etc
  • add the required tools from the toolshed
  • add your local (non-toolshed) tools
  • try whether it works....

I have done this kind of approach last year. Though, I only had to switch from (mercurial) version 15.10 to (git) version 16.04, but it involved a hardware change and system software change.

Whatever way you gonna try, make sure you have a solid backup of both the complete galaxy directory tree and the (PostgreSQL) database.

Hope this helps Hans-Rudolf

ADD COMMENTlink written 5 months ago by Hotz, Hans-Rudolf1.8k

Hi Hans-Rudolf,

The galaxy version we have was from May, 2012 release. I like the different approach you proposed and is going to use it for our galaxy update. Thanks a lot for your suggestions!

The new installation of galaxy is going to be in the same server as the old one, but will be in a different directory. We use MySQL database instead of PostgreSQL. I think the manage_db.sh script should work for both. We will do following:

(1) git clone the current release of galaxy in a new directory on the server (2) create a new mysql database and copy existing galaxy mysql database to the new one (3) create a new apache virtualHost as the web host for the new galaxy (4) modify galaxy.ini and make it use the newly created db (5) run 'manage_db.sh upgrade' (6) link new galaxy 'database' directory to the existing galaxy database directory (7) make changes for *.loc files and all configuration files as needed for the new galaxy. (8) stop old galaxy instance and start the new one

We have huge amount of galaxy datasets accumulated from last 6 yrs usage and no backup is available for them. I assume the new galaxy installation won't modify any preexisting datasets in the database directory (step 5), so we can keep using the existing galaxy if the new installation fails, is it correct?

Thanks again for your expertise!

Jane

ADD REPLYlink written 5 months ago by janecao9990

Hi Jane

two comments first:

Your plan looks good, except: you need to 'stop old galaxy instance' before you 'copy existing galaxy mysql database to the new one'. Otherwise, if the old server is still used, you run into problems with datasets out-of-sync with the new mysql database.

Yes, you are right, the new galaxy installation won't modify any pre-existing datasets.

Good luck Hans-Rudolf

ADD REPLYlink written 5 months ago by Hotz, Hans-Rudolf1.8k

Hi Hans-Rudolf, Thanks again for your help! Yes, I will 'stop old galaxy instance' first.

Jane

ADD REPLYlink written 5 months ago by janecao9990
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