galaxyproject / galaxyproject/tools-iuc
File extension causes error when extracting reads from SRA archive in current history
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- Avg merge
- 23h 54m
- Merged PRs (30d)
- 59
Description
The following line directly store the file name as `acc`.
https://github.com/galaxyproject/tools-iuc/blob/86211daa63a6f39524df8759364795b782324303/tools/sra-tools/fasterq_dump.xml#L14
This works fine when the uploaded SRA file has no extension aka '.sra'. However, with extension the following line would fail at capturing the output files. Because `fasterq-dump` tends to only include the sra id in its output files and only generates files like `SRR000000_1.fastq` and `SRR000000_2.fastq`.
https://github.com/galaxyproject/tools-iuc/blob/86211daa63a6f39524df8759364795b782324303/tools/sra-tools/fasterq_dump.xml#L45-L46
Maybe the upstream code could remove the file extension for `acc`, so the symlink down here won't have the '.sra' (tried to tweak the code by myself but ended up getting strange errors)
https://github.com/galaxyproject/tools-iuc/blob/86211daa63a6f39524df8759364795b782324303/tools/sra-tools/fasterq_dump.xml#L15
Contributor guide
Research direction
Open tools/sra-tools/fasterq_dump.xml at lines 14-15 and 45-46, then reproduce the extraction with an uploaded .sra file. Compare the archive name with the fasterq-dump outputs SRR000000_1.fastq and SRR000000_2.fastq; done means the wrapper captures those files when the input has an extension.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- xml
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 52/100