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How to set PATH to OrthoFinder2 correctly? #22
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Hi Jan, Many thanks for your feedback. So far, Please also make sure you have DIAMOND installed as executable tool ( Does this work for you? Best wishes, |
Hi Hajk, Many thanks for your quick response! Unfortunately, this still doesn't seem to work for me and I get the error:
I'm in a macOS environment and my path to OF2 appears to be Is there maybe a way to set a custom path in Many thanks in advance for your help! Jan |
…ir own orthofinder path (Many thanks to Jan Strauss) #22
Hi Jan, Thank you very much for coming back to me and for this great feature request. I now added a new The only problem that I still see is that you cannot pass the I will see if I can find a way around this so that users can also set the I hope this helps? Many thanks, |
Hi, when I try to set the dNdS functions param ortho_detection to "Orthofinder2" I get the error "Error: Please choose a orthology detection method that is supported by this function." Is there something else I should be doing? Or is this not included in the dNdS function? |
Hi @mcatto Thank you for your question. Unfortunately, dNdS with orthogroups is not supported yet. It is on my long ToDo list, but it may require a while until this feature is available. I hope you find pairwise dNdS useful anyway. Cheers, |
Hi @drostlab,
I'm trying to set up
orthologr
for detection of orthologs in multiple species.I've installed
orthofinder
into my PATH usingconda install orthofinder
.Calling
orthofinder -h
fromterminal
showsOrthoFinder version 2.4.0 Copyright (C) 2014 David Emms
suggesting thatorthofinder
is installed correctly.Yet, I still run into the following issue when running the example code:
How should I setup
orthofinder
correctly?Many thanks in advance for your help!
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