Moving Galaxy workflow from one galaxy instance to another instance

Question: Moving Galaxy workflow from one galaxy instance to another instance

2.1 years ago by

Hello,

I want export workflows from one galaxy instance(old) to another galaxy instance(new). Many tools are locally developed and installed from local galaxy toolshed in old galaxy instance. In the new galaxy instance, new local toolshed IP/address is different. So the tools installed from local toolshed has different id (e.g. old ids 10.xx.xx.xx/aa/bb/. new ids 128.xx.xx.xx/aa/bb/).

And, I have copied the workflows to new galaxy instance.

Now, due to different tool Ids, even though the tools are there in the new galaxy, the workflows are complaining about "missing tools".

Basically, I have to replace the old address by new address in the backend.

There are so many tables in postgress. I checked/tested some of the tables and it doesnt work.

Any suggestions?

Jeevan

import toolshed workflow tools export • 768 views

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modified 2.1 years ago by Dannon Baker ♦ 3.7k • written 2.1 years ago by jeevan.karloss • 0

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Adjusting the paths to tools in the database will be a complicated endeavor. A direct approach will ensure that Galaxy functions correctly.

Your goal is to have the workflow match the tools.

It is not clear if the workflow uses the "old" or "new" tools. If the workflow uses old tools, the workflow will probably need to be recreated on the updated Galaxy instance to use the new tools. If the workflow uses new tools and these are in your toolshed, removing the "old" tools and installing the "new" tools that match the workflow is likely the best solution. If not in the toolshed yet, they should be added first.

Thanks, Jen, Galaxy

ADD COMMENT • link modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

2.1 years ago by

jeevan.karloss • 0

jeevan.karloss • 0 wrote:

Ok. Thanks.

Is there any database schema diagram for the galaxy database?

Jeevan

ADD COMMENT • link written 2.1 years ago by jeevan.karloss • 0

Have a look here: https://galaxyproject.org/schema/SchemaSpy/index.html

You cn also create this page yourself with SchemaSpy (http://schemaspy.sourceforge.net/), to make sure to get the schema corresponding to your local database.

Regards, Hans-Rudolf

ADD REPLY • link written 2.1 years ago by Hotz, Hans-Rudolf • 1.8k

2.1 years ago by

jeevan.karloss • 0

jeevan.karloss • 0 wrote:

From which table, Workflows fetch the tool path? I checked many tables manually based on the table names. Stil. I am not able to modify the workflow tool paths.

ADD COMMENT • link written 2.1 years ago by jeevan.karloss • 0

2.1 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

I'll let others follow up on how to fix your tools, but I can help with the image version of a current schema reference I just generated:

ADD COMMENT • link written 2.1 years ago by Dannon Baker ♦ 3.7k

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