README.md

Docker container for the guide-seq package

This is a docker image for the GUIDE-Seq implementation from Tsai lab.

Usage

docker pull ghcr.io/zethson/guide_seq:latest
docker run --rm -it ghcr.io/zethson/guide_seq:latest /bin/bash

The executable to start the workflows is guideseq.py.

Testing

Inside the container run

git clone https://github.com/tsailabSJ/guideseq
cd guideseq/test
guideseq.py all -m test_manifest.yaml

Building a singularity image

Often times singularity images are prefered over docker images to be able to run them in a HPC environment. You can build one by running

mkdir -p /tmp/singularity_output

docker run -v /var/run/docker.sock:/var/run/docker.sock \
-v /tmp/singularity_output:/output \
--privileged -t --rm \
singularityware/docker2singularity \
ghcr.io/zethson/guide_seq:latest

Now you can find your shiny new singularity image in /tmp/singularity_output