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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
54 stars 14 forks source link

Error: Install the "PEPATACr" R package before proceeding. #275

Closed DavideBrex closed 6 months ago

DavideBrex commented 6 months ago

Hi, thank you for this nice tool.

I am trying to run the tutorial (http://pepatac.databio.org/en/latest/tutorial/) using the singularity image. However, the execution stops, and I get an error related to PEPATACr: Error: Install the "PEPATACr" R package before proceeding. PEPATAC_log (copy).txt I checked, and the R package is installed inside the container. I also installed it on my local machine but still I get the same error.

Thank you for your support. Best,

Davide

nsheff commented 6 months ago

@DavideBrex -- were you able to solve the problem?

DavideBrex commented 6 months ago

yes, there was an issue with my local installation of PEPATACr on my local machine. Now it works. Still, I did not manage to set singularity to use the R libraries within the container instead of my local ones. I tried to add the "-e" flag to the singularity arguments, but it did not work.