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bailey-lab / MIPTools

A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
https://miptools.readthedocs.io
MIT License
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Wrangler app bad substitution error #37

Closed arisp99 closed 2 years ago

arisp99 commented 2 years ago

Bug Description

In #26, we implemented checks to ensure that arguments passed to the wrangler app had no spaces in them. Our solution relies on parameter expansion. Crucially, this is a non-POSIX feature. While our container does run using bash, this error would indicate that the parameter expansion is not working properly.

Reported by @iek.

arisp99 commented 2 years ago

Not being able to perform parameter expansions causes errors in other places as well. The lines that need to be fixed are: https://github.com/bailey-lab/MIPTools/blob/d3e613ccababf5526f106039a07e3f9f9aa3c00c/MIPTools.def#L409-L420