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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Issues with ArchR calling MACS2 from WSL in Windows Environment #2231

Open joeyQX opened 2 weeks ago

joeyQX commented 2 weeks ago

escription: I'm trying to run ArchR's peak calling functionality on Windows using MACS2 installed in WSL. While MACS2 is successfully installed and running in WSL (confirmed with macs2 --version), ArchR fails to locate and execute it from the R/RStudio environment.

Current Setup:

What I've tried:

  1. Setting MACS2 path in R: pathToMacs2 <- "wsl macs2" pathToMacs2 <- "/usr/local/bin/macs2" pathToMacs2 <- "wsl.exe macs2"

    return all not found

Confirming MACS2 installation in WSL: bash: which macs2 # returns /usr/local/bin/macs2 macs2 --version # works correctly

rcorces commented 2 weeks ago

Hi @joeyQX! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

joeyQX commented 2 weeks ago

Hi @joeyQX! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

Thanks, hope your future reply!

immanuelazn commented 1 week ago

Hi joey, pretty sure this is a nuanced question on how $PATH is set, and where it happens with respect to when you execute your wsl command from windows. Have you tried this as a test from R? system("wsl /usr/local/bin/macs2")

immanuelazn commented 22 hours ago

Hi joey, are you still having issues with ArchR?