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TCP-Lab / x.FASTQ

Bash wrapper modules for the remote analysis of RNA-Seq data, with persistency features.
MIT License
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`x.fastq -r` command crashes when it doesnt find the searched version pattern #15

Closed Feat-FeAR closed 8 months ago

Feat-FeAR commented 8 months ago

The x.FASTQ -r command does not seem to pickup metaharvest, but x.FASTQ -l does work. I'm not sure why.

This is simply because the for loop in x.fastq.sh that collects the versions of all the modules breaks down before it gets to the harvester... and this is due to the fact that it is an implicit requirement of ALL x.FASTQ scripts to have somewhere a versioning line of the type

ver="x.y.z"

It may well be a comment, but it has to be there. See here, for instance:

https://github.com/TCP-Lab/x.FASTQ/blob/299b544fb94a8596ebc4652d098fbfecc5f5b44d/cc_assembler.R#L17-L19

I've added versions for all the scripts, so this is fixed, but it might be nice to not have the script fail if they are not present, but this is for another PR.

Originally posted by @MrHedmad in https://github.com/TCP-Lab/x.FASTQ/issues/8#issuecomment-1988039584

Feat-FeAR commented 8 months ago

Fixed by commit a39dbcddfc56b6c892d6b5e88339f6bc7e0e0f70. Thank you @MrHedmad for pointing it out.