How to visualize structure figures as a Mac M1 chip user

[Elizabeth Collins]

Hello structure community, 

I am at my wit's end with trying to visualize my structure output files! I ran structure on a high-performance cluster, so didn't have problems producing the files. But I absolutely cannot get any of the following programs to work on my Mac M1 chip (Monterey): structure GUI version, distruct, or clumpp. 

I have come to understand that I am not alone in this incredibly frustrating problem, and it isn't likely that I am going to be able to fix it. I am not a computer programmer and it sounds like even if I was I have seen people on here are saying that these software packages simply can't be run on a Mac M1 chip. 

So how are all the Mac M1 people visualizing structure files and running distruct and/or clumpp? Are there R packages you have had success using? Or should I just go get a windows machine somehow? I am very new to R so this would not be my first choice, but I do need to learn how to use R... 

Thanks for any insights you all have!

Betsy Collins

PhD candidate, George Mason University

[Vikram Chhatre]

Hi Betsy,

George Mason has HPC Resources. You can apply for an account here: https://orc.gmu.edu/new-user-information/

Since HPCs run on some flavor of Linux (x386 platform), you should be able to run STRUCTURE, Distruct and Clumpp there.  Additionally, you can use Structure_Threader or StrAuto to automate your STRUCTURE runs.

For making bar plots, one option is https://distruct2.popgen.org. It should run on a M1 mac.

If you run into issues, let us know.

V

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[Kristopher Wojtusik]

Hello,

Just wanted to add one more option to the visualization list. I'm not sure how others feel about it, we always use Clumpak in our lab and it has always worked well for us. There's no programming or code writing involved, so if you'd rather code it then Vikrams options are probably better, but clumpak is super straightforward and easy to run. 

Hope it helps.

-Kris

To view this discussion on the web visit https://groups.google.com/d/msgid/structure-software/CAJZnH0m_tFxW0_ORxt9bBZN_mbETejUWnzDo4RdvOoUABfS4hg%40mail.gmail.com.

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Kris Wojtusik

Graduate Research Assistant

Department of Biological Sciences

University of New Hampshire

kwojt...@gmail.com

603-583-1928

[Elizabeth Collins]

Thanks so much for your very fast reply, Vikram! 

I have been successfully running structure on GMU's cluster, but can I actually make plots from the command line? For some reason I was under the impression I couldn't (but I am a very new user to structure). 

Good idea about using Clumpp on the cluster - I will ask them to install it. I am assuming the cluster version allows for plots of the data to be made, right? 

Thank you so much for the new version of distruct! I am about to try to run it now.

Thanks again, 

Betsy

[Vikram Chhatre]

Note that the distruct I linked (https://distruct2.popgen.org) is not a new version of the Distruct you know (https://rosenberglab.stanford.edu/distruct.html). They are different programs. You should be able to use the former on your M1 mac since it's a Python script. You can also look up clumpak as suggested by Kris.

I personally always do all the plotting on my mac and run all the analyses on the HPC.

V

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