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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

Singularity Issue #212

Open e-arslan opened 2 years ago

e-arslan commented 2 years ago

Hi,

I am trying to use the singularity version on the HPC platform, yet got the "FATAL: permission denied" error. Checking pepatac.py is not an option as pypiper module is missing and the HPC platform does not allow to install new modules manually.

I run the following code:

 singularity build pepatac docker://databio/pepatac:latest
 singularity instance start -B /rsrch3/home/genomic_med/earslan/:/rsrch3/home/genomic_med/earslan/ pepatac pepatac_instance
 singularity exec instance://pepatac_instance \
 /rsrch3/home/genomic_med/earslan/pipelines/ATAC-Seq/pepatec/src/pepatac.py ...