How to run CallPeaks()

Question

[Chris]

Hi all,

Would you suggest how to fix this in R? MACS2 is an independent tool I can load and run in the terminal, but not an R package.

peaks <- CallPeaks(pbmc)

Error in CallPeaks.default(object = allfragpaths, macs2.path = macs2.path, : MACS2 not found. Please install MACS:https://macs3-project.github.io/MACS/

I run this pipeline: https://stuartlab.org/signac/articles/pbmc_multiomic (edited) Thank you so much!

To run macs2, I use terminal ml macs2. I got an error (language ca is not supported ...) when type reply so I add to the post.

[rfran010]

How are you running this? I believe it essentially searches your PATH for macs2 command. If you can run macs2 from the command line, it should work.

[Chris]

To run macs2, I use terminal ml macs2. I got an error (language ca is not supported ...) when type reply.

[seidel]

Have you tried running ml macs2 prior to running your R Script, so that macs2 is available in the same environment your R script is running in?

[seidel]

But are you launching RStudio from a command-line? Or are you connecting to via a web browser? The terminal tab within RStudio will have different properties than the terminal outside of RStudio. If you are launching RStudio from a command-line, I'm wondering if you can load the module prior to launching RStudio. If you're using RStudio Pro, there may be a fix.

[Chris]

Thank you for your reply! I run via a web browser and I don't use RStudio Pro. I try to load macs2 on the terminal inside and outside RStudio and still got that error. One tab for the terminal and one tab for RStudio.
Update: CallPeaks(pbmc,macs2.path="/../macs2/2.2.71/bin/macs2") will work.

[Chris]

Yes, I click to terminal in my Rstudio and run ml macs2. I am using a server and seem the R environment doesn't connect with the environment that runs macs2.