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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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installing ArchR on conda #2146

Open Mashazhefer opened 6 months ago

Mashazhefer commented 6 months ago

Hey! I've been having serious problems installing ArchR on Conda. I've added the YAML file and shown the outputs of a failed installation. I've tried running this on multiple versions of R (3.5, 3.6, 4.1.3, 4.3.0, 4.3.3,4.2.0). ive tried intalling with devtools, remotes, and other ways.

install.packages("ArchR") Installing package into ‘.../R/x86_64-conda-linux-gnu-library/4.2’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘ArchR’ is not available for this version of R

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages Warning in install.packages : converting NULL pointer to R NULL

Note that I didn't change the prefix in line 425. moshe.zip

rcorces commented 6 months ago

Hi @Mashazhefer! 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.

Mashazhefer commented 3 months ago

thought it would be valuable to upadte success:

  1. ran macs2 not on R (wsl directly -> .narrowPeak output file), and filtered out nonstandard chromosomes(chrM etc.)
  2. used GenomicRanges lib to process the .narrowPeak file
  3. ArchRProj <- addPeakSet() (manual 10.1.7)
  4. ArchRProj <- addPeakMatrix()

hope this is helpfull for whoever couldnt run macs2 through R. id be happy to upload the R script, if anyone finds it usefull