Freebayes stopped working in exome analysis

usegalaxy.org support
1

Hi I am teaching a class using galaxy. We are running the exome analysis of a genetic disease tutorial. Wen we get to the variant call step with FreeBayes we get an error. The error says Freebayes not found.

The same history works when imported to usegalaxy.eu - so my guess is something went wrong with freebayes on the .org server.

Here’s a link to my History

https://usegalaxy.org/api/short_term_storage/6c6c28fe-58f4-4146-8848-1030a018b548

2

Hi @Ken_Saville

It can be an installation issue with the latest version. Thank you for reporting it! Ping @jennaj - issue with the latest FreeBayes.

Try an early version, for example, I don’t see any issue with Galaxy Version 1.3.1. Users can change version of a tool during job setup via Version (three blocks) icon in the top right corner of the middle panel.

BTW, the history link it is to a zipped archive. Some people might be uncomfortable with download of zip files. Maybe consider the following procedure: History options (three horozontal bars) icon at the top right corner of the History panel > Share or Publish > Make history accessible in the middle window > Copy the URL and share it.

Kind regards,
Igor

1 Like
3

Great, thanks for reporting and figuring out a workaround, I’m reviewing now, more soon.

Update

Hi @Ken_Saville I’m not able to reproduce a problem with the tool not being found. This is my test history.

I ran the two most current versions of Freebayes at the EU server first, then generated a history archive, moved that over to the ORG server, and reran both there too. I used a very simple tool test that will not hit every tool option but I don’t think that will matter based on how you explain the problem.

My guess from here: you were using some older version of Freebayes that is available at the EU server, and that one is not available at the ORG server for some legacy reason.

What to do:

  1. When working directly: use a more current version of Freebayes at both servers.
  2. When using a workflow: after importing the workflow at the server where you want to run it, open the workflow in the Workflow Editor.
  • When possible, tools in your workflow will “map over” to the version available at that server. You’ll get a pop-up message reporting what exactly what changed.
  • This might disturb some tool parameters – but there will be a message in the pop-up alerting you about these, too, if any.
  • If a tool is completely not found – when working at a public server, you can let us know and we can check why and maybe address that. When working at your own server, there are ways to automatically add tools associated with workflows in a batch.
  • Note: we probably won’t be adding in really old versions of tools if there are current versions available. The solution here is to update the workflow, then maybe republish that at WorkflowHub or wherever you are working.

Please check to see if my guess is correct, and please let us know if you need more help or if this is resolved. :hammer_and_wrench:

Next time, or this time if you want more followup, please use the share link function for data review. @igor is correct a history share link is a better choice for feedback here. See → FAQ: Sharing your History

4

Hi @jennaj ,
Maybe it was a temporary issue. The latest FreeBayes has failed for me couple days ago: Galaxy
The same version, as in your test.
Gave a great day,
Igor

1 Like
5

I see … your error is about the tool itself and a few of the dependencies not being found! Odd but seems resolved for you too. I like things that fix themselves, ha :upside_down_face: