galaxy-set-metadata: command not found

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galaxy-set-metadata: command not found #13446

Closed jeanetx closed 2 years ago

jeanetx commented 2 years ago

This has been happening over the past two weeks. I upload a 3 column bed file (no header) as I usually do. The file is sorted by chr start stop. The attributes of the uploaded bed file is set to bed. When I run Merge overlapping regions, I get the following error on the output file:

When I set the attributes of the output file to bed file, the job that trys to auto-detect the attributes will run forever (a previous attempt ran for >1 week).

mvdbeek commented 2 years ago

Thanks for the report, this currently affects some very old tools that we keep installed for reproducibility (@natefoo, can you take a look at this ?). For the time being please use https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0 to merge intervals.