"TEtranscripts annotates reads to genes and transposable elements (Galaxy Version 2.2.3+galaxy0)" this latest version does not operate.

Dear specialsits,

“TEtranscripts annotates reads to genes and transposable elements (Galaxy Version 2.2.3+galaxy0)” constantly fails, with the error message below, even with the test dataset provided by the original authors of the tool.

|Tool Standard Output|*empty*|
|Tool Standard Error|/data/jwd04/main/054/935/54935546/tool_script.sh: line 10: TEtranscripts: command not found|
|Tool Exit Code:|127|
|Job Messages|* { "code_desc": "", "desc": "Fatal error: Exit code 127 ()", "error_level": 3, "exit_code": 127, "type": "exit_code" }|

on the other hand

TEtranscripts (Galaxy Version 2.2.1+galaxy0) works on every dataset that failed on Version 2.2.3, including test data.

I would like to draw your attention to the issue with the latest version, as it may make people loose time trying to work on it. I can provide you the histories of failed work, if needed.

Thanks a lot for the great work you do by running and maintaining the Galaxy platform.

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Welcome @qcsciphi

That would be great. Please send in a bug report from the application to the admins of the EU server. Include a link to this topic in the comments section for context. Leave all datasets undeleted please.

When tools error with a message like command not found it sometimes means that the tool could not read the inputs. This could be a format, content, or datatype issue.

How to reproduce the tool tests in Galaxy:

  1. Find the tool repository linked at the top of the form → this is for the current version and can be navigated by version: https://toolshed.g2.bx.psu.edu/view/iuc/tetoolkit_tetranscripts/8e96d712a2bd
  2. That view links out to the full development repository. The xml for the tool includes tool tests near the end, and the matching test data is in the dev repo.

Maybe try with that specific test data to see what results? Or maybe compare the format to that of the original author’s test data? Sometimes the differences in “expected” format can vary slightly between the command-line version and the Galaxy version. And, command-line uses file extensions as a metadata but Galaxy uses “datatype” metadata (not always a match for file extensions).

I’ll try to run that same test to see what happens but it will be later this week and it sounds like you understand how this tool works, so some help is appreciated. Let’s also bring in @gallardoalba since he is a lead tool developer – he may have more insight plus is part of the EU core team should the issue be server specific and not really about the wrapper.

Thank you for reporting the problem! Very helpful to get so many details

Dear Jennifer,
Thank you for your kind reply with helpful comments and suggestions.
I already created a bug report from the tool, including a link to access the history.
Hope that the latest version of the tool will also be running as the previous versions and provide service to future users.
Thank you and all your colleagues for the great job you do.

1 Like