Question: Local instance upgrade caused error: need to upgrade database from 132 to 134
0
gravatar for deane
3 months ago by
deane30
deane30 wrote:

I recently updated a local instance of Galaxy to revision_17 using git checkout release_17.05 && git pull --ff-only origin release_17.05

Now the instance will not run, telling me I need to upgrade the database from 132 to 134 after I backup. I am using the default database (sqlite/alchemy?). How do I backup the database? Then how do I update to 134?

Any help will be appreciated.

Thanks, Deane Blazie

admin git upgrade local 17.05 • 190 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by deane30
1

What version of Galaxy are you upgrading from?

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson23k

I don't know how to find the current version I updated from because it won't run. But it was installed around June 2016. I'm running on Linux.

Thanks for the help.

ADD REPLYlink written 3 months ago by deane30

Hi Deane

Have a look at the file "version.py" which is lists the version number. Go into the galaxy root directory, and execute: "cat lib/galaxy/version.py"

Hope this helps Regards, Hans-Rudolf

ADD REPLYlink written 3 months ago by Hotz, Hans-Rudolf1.7k

Because I have already done the git upgrade, the version.py file shows 17.05. So I don't know what version I came from but I'm guessing 16.07

My question is this: How do I backup the existing database. The links all show how to upgrade the database with the manage_db.py script but now how to backup the database. I've looked on the web at sqlite alchemy but can't find much there either. Is there a database manager that has the tools to unload a database and reload with the new schema?

Thanks again, Deane

ADD REPLYlink written 3 months ago by deane30

Yes, I'm trying to find instructions on how to backup the existing database. Then I can update the database with manage_db.py. But first I need to unload it, back it up.

Thanks, Deane

ADD REPLYlink written 3 months ago by deane30

The admin docs have help, but this prior post also covers the details in a conversational format. https://biostar.usegalaxy.org/p/11858/

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The database is going to need to be upgraded. You'll need a backup to start from.

The June 2016 date indicates you started with the 16.04 release, but it could have been earlier (16.01 or even prior). I'm not sure which used the schema version 132 but will ask for some feedback from the developers.

How-to: https://galaxyproject.org/admin/get-galaxy/#keep-your-instance-backed-up

Release notes: https://docs.galaxyproject.org/en/master/releases/

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson23k
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