Docker and Singularity container for iPsychCNV

iPsychCNV (https://biopsyk.dk/ipsychcnv/) is an R package software capable of finding copy number variation in amplified DNA from dried blood spots on Illumina SNP array.

This is to show how to run iPsychCNV via Docker and Singularity containers

You can directly pull the container

docker pull bayramalex/ipsychcnv:latest

alternatively you can download repo and build via dockerfile as

docker build -t ipsychcnv .

Then you can run the container as

docker run ipsychcnv <options> .

Singularity container can be directly built via Docker container as

singularity build ipsychcnv.sif docker://bayramalex/ipsychcnv:latest 

and run it as

singularity shell --no-home ipsychcnv.sif 

R -e “library(iPsychCNV); LongRoi <- MakeLongMockSample(CNVDistance=1000, Type=c(0,1,2,3,4), Mean=c(-0.6, -0.3, 0.3, 0.6), Size=c(300, 600))”

You can also run this container as sandbox (https://sylabs.io/guides/3.0/user-guide/build_a_container.html#creating-writable-sandbox-directories)

singularity build --sandbox new.sif ipsychcnv.sif
singulairty shell --no-home --writable new.sif

More iPsychCNV specific commands