Awesome

Singularity image of aCNViewer

The docker image of aCNViewer is not working with Singularity without sudo because several files have read/execute permissions only for the file owner (root). This repository hosts a very simple Singularity definition file that bootstraps the docker image and assigns the same permissions of the file owner (u) to the other group (o) for the folder containing aCNViewer scripts and data (/data) by doing:

chmod -R o=u /data/

The Singularity image is build automatically by Singularity hub and can be download with:

singularity pull shub://IARCbioinfo/acnviewer-singularity

Then aCNViewer can be run, for example to generate histograms from ASCAT-like input file (https://github.com/FJD-CEPH/aCNViewer#othercnvformats):

singularity exec acnviewer-singularity_latest.sif python /data/aCNViewer/code/aCNViewer.py -f input_cnv.txt -t acnviewer_output --refBuild hg38 -b /data/aCNViewer_DATA/bin/

Note that other modes of aCNViewer have not been tested.

Reference: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189334