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Question: extract workflow from a history
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gravatar for hudiejie
4.1 years ago by
hudiejie • 20
Singapore
hudiejie • 20 wrote:

Hi, I encounter a problem when I tried to extract workflow from a history. pls refer to:

GURU MEDITATION: #fc33f2d54e8e4ea4a3d4ae731380816e
rna-seq • 869 views
ADD COMMENT • link •
modified 4.1 years ago by Dannon Baker ♦ 3.7k • written 4.1 years ago by hudiejie • 20

Is this an error? Can you please give more information?

ADD REPLY • link written 4.1 years ago by Bjoern Gruening ♦ 5.1k

This is an internal error that gets thrown extracting the workflow.  I'm looking into what's happening here now, but it has to do with the extraction of a step containing repeats.

ADD REPLY • link written 4.1 years ago by Dannon Baker ♦ 3.7k
2
gravatar for Dannon Baker
4.1 years ago by
Dannon Baker ♦ 3.7k
United States
Dannon Baker ♦ 3.7k wrote:

This is an internal error that gets thrown extracting a cuffdiff step that you had in that particular history.  The problem is that values weren't found for the conditions or replicates due to it being an old version of the tool wrapper, 0.0.5, which is no longer available on the server.  Basically, the available tool wrapper versions expect parameters the version at the time you ran this did not have, so Galaxy doesn't know how to map parameters to your tool in the workflow it's trying to create.

This should definitely be handled a little better by the extract code, but since that's going to be a code fix on our end you may want to re-try extract and leave the cuffdiff step unchecked.  You can edit the newly extracted workflow at that point and add it back in.

You could also re-run the cuffdiff step (with the newer version of the tool -- you'll see what I mean), and then re-extract but make sure to check the *new* cuffdiff step and *not* the old one.
ADD COMMENT • link written 4.1 years ago by Dannon Baker ♦ 3.7k

Yes! The problem is caused by the tool version difference between now and previously, which is also warning behind each tool, like: Dataset was created with tool version "0.0.5", but workflow extraction will use version "0.0.6".  

Thanks for helps.

ADD REPLY • link written 4.1 years ago by hudiejie • 20
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