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I think this is a great idea, but would also like to fall back on bundling a version of salmon that works with PISCES. Some of the older versions (< 1.0) are incompatible with genome-centric transcriptome indexing. I'll consider how this might be implemented.
Path to Salmon binary is now hardcoded. It would be better when PISCES would check if salmon is in the PATH eg. like here https://stackoverflow.com/questions/377017/test-if-executable-exists-in-python.
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