galaxyproject / galaxyproject/training-material
STARsolo 2.7.5b (Tutorial Feedback #989 Oct 29th 2020)
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Description
looks like there are two independent issues here:
(ping @jennaj @mtekman @blankenberg )
- Yes, Homo_sapiens.GRCh37.75.gtf is not correctly auto detected as 'gtf' when uploaded from zenodo. I have seen this before (on other occasions), and it needs a fix in the sniffer (probably more than just a 'paper cut'?)
- STARsolo 2.7.5b (the current default on usegalaxy.eu) is broken (or need a different kind of transcripts annotation file?). The same inputs work with a previous tool version (e.g.: 2.7.2b1 )
Contributor guide
Research direction
Reproduce both reported cases using the Zenodo upload of Homo_sapiens.GRCh37.75.gtf and the STARsolo 2.7.5b workflow on usegalaxy.eu. Start by examining the file-type sniffer and the tutorial's STARsolo inputs, then compare behavior with version 2.7.2b1. Done means the annotation is detected as GTF and the current workflow either runs with the documented inputs or clearly identifies the required annotation format.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100