Editing reference genome for TopHat on Trapline

Question: Editing reference genome for TopHat on Trapline

2.8 years ago by

d.prince • 10 wrote:

I am trying to use the Trapline workflow for RNA-Seq data, and have read the manual. I want to edit the reference genome that TopHat uses from the predefined mm9 to my study species whose genome is saved in my history. I have used the workflow editor to change the TopHat settings, and then saved the workflow. When I come to run the workflow the settings for TopHat have reverted to mm9 again. I'd appreciate any advice on how to solve this issue.

Thanks,

David

rna-seq workflow trapline • 869 views

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modified 2.8 years ago • written 2.8 years ago by d.prince • 10

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There are some known issues with workflows and reference genome selection captured here:

https://github.com/galaxyproject/galaxy/issues/1132

To my knowledge, all of these issue have not been fully resolved yet. Your case seems to be related but distinct, in short: "Target reference genome edits for Tophat within the workflow editor are not saved"

Is this true? If so, then we can add that case to the existing issue or possibly create a new one. If you would share an example history and the workflow (edited), this can be confirmed. Replicate the case at http://usegalaxy.org (if working elsewhere), generate the share links, then send the links along with a link to this post to galaxy-bugs@lists.galaxyproject.org.

We'll also run a quick test here, but using your exact data could reveal other factors/clues about what is triggering the problem.

Thanks for reporting the problem, Jen, Galaxy team

ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi again, I could mention the work-around:

1. execute the workflow step-by-step, from the point where the first workflow issue is encountered, in the history.

2. exact a new workflow so that it includes only the steps/tools with the correct reference genome assignment

Our team is reviewing the other items again plus your case. Some changes will likely involve tool wrapper updates, which complicates the solution.

ADD REPLY • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hello,

An independent test with Tophat included in a workflow shows that it is possible to change/save the reference genome and have that change persist at runtime. The test was performed at http://usegalaxy.org.

There were some issues on the server over the last few days. Maybe try this again and see if you are still having the same problem?

If this is occurring at some other Galaxy server then it could be that the code is not up to date or some other issue (configuration) is a factor. This would apply to your own local/cloud Galaxy or private/public shared instance.

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

2.8 years ago by

d.prince • 10

d.prince • 10 wrote:

Thanks Jen for your responses.

Here are some more details that hopefully will help locate the problem. I am using an account at http://usegalaxy.org. The problem is independent of my data, as I haven't run any of it through the workflow. The workflow that I am trying to edit is a published workflow called RNAseqTRAPLINE that I imported from the Galaxy website.

In case it was a problem with the server I have started again from scratch today. I re-imported the workflow and used the workflow editor to try and edit the instances of TopHat in RNAseqTRAPLINE, changing from "use a built-in genome" (mm9 in this instance) to "use a genome from history". I then saved. During saving I received the server error "Duplicate workflow outputs with name [out_file1] found", and I clicked on ignore. I then ran the workflow (and was asked if I wanted to leave the page or stay on the page, to which I clicked leave the page). The workflow then appears, but when I click on the steps involving TopHat (e.g. Step 30) it states that it will "use a built-in genome" (mm9), and therefore my edits have not been saved.

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