Workflow extraction issue

workflow
workflow-extract

#1

Hi all,

I am trying to extract workflow from history, but Galaxy generates error, how can I overcome it?
Error text is below.

# Internal Server Error

## Galaxy was unable to successfully complete your request

An error occurred.

This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

The error has been logged to our team. If you want to contact us about this error, please reference the following

GURU MEDITATION: #7aebb984889f4a68b05f86a3448609bc


#2

Sorry you ran into a problem. Two things to try first:

  1. Try extracting the workflow again, now, to test if this was a transient server issue.
  2. If the error occurs again, please generate and send in a history share link in an email to galaxy-bugs@lists.galaxyproject.org.

How to: Sharing and Publishing your work

Be sure to mark history objects as accessible when creating the link by clicking on the small checkbox next to the “Share by link” button. You can unshare and re-share if this history was already shared but the objects/datasets were not. The mailing galaxy-bugs list is private to the usegalaxy.org server admins and your data will not be exposed publically.

share-link-with-shared-objects


#3

Thank you for quick reply. Please follow the link here https://usegalaxy.org/u/hov/h/3rd-whole-exome ,
because Galaxy says that "galaxy-bugs@lists.galaxyproject.org is not a valid Galaxy user." Please see the picture.


#4

OK, thanks for posting the share link.

The original intent was to send the share link in an email to the galaxy-bugs mailing list, not to share it directly as one would with another user on the server.

I’ve got the link now. If you want to keep your history private, you can edit your post here to remove it. Anyone will be able to see it when posted here publically. It would have remained private if sent via email to the mailing list.

More feedback about the reasons why the workflow extraction failed once we review.


#5

Thank you, looking forward for your feedback.


#6

Hi - We are still reviewing to find out exactly why there is a workflow extraction problem with this history.

However, it appears that the datasets in the history were moved/combined from other analysis histories. This is likely a factor leading to the workflow extraction problem. When test extracting a workflow in the current history, I can get as far as including all steps up until the trimmomatic job (and excluding the rest). Excluding the trimmomatic job is not enough, and would leave out that step in your workflow anyway.

Try running the analysis in a single history, leaving contiguous jobs/steps/datasets active, then extracting a workflow.


#7

Thank you, I will try