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jtlovell / GENESPACE

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BUG when specifying rawOrthofinderDir #157

Closed dmacguigan closed 2 months ago

dmacguigan commented 3 months ago

Hello,

I am attempting to use previously generated OrthoFinder results with GENESPACE. However, I noticed that line 84 of run_genespace.R does the following:

gsParam$paths$rawOrthofinder <- gsParam$paths$orthofinder

This means that no matter what the user specifies for the rawOrthofinderDir option when running init_genespace, the run_genespace function will always use the default OrthoFinder results directory (file.path(wd, "orthofinder")).

Once I matched the expected directory structure (copied my prior OrthoFinder run into "wd/orthofinder"), the run_genespace function proceeds correctly and does not attempt to rerun OrthoFinder.

jtlovell commented 2 months ago

Thanks! Appreciate this report, and have added it to my notes.