Run ViewBS with `Docker` or `Singularity`

Docker

docker pull pulls an image or a repository from a registry

docker pull xie186/viewbs
## Use "docker run <image name>" ViewBS" to replace "ViewBS". Here is an example:
cd ViewBS_testdata/
docker run -v ${PWD}:/data -w /data bc1743f3418f ViewBS MethOneRegion --region chr5:19497000-19499600 --sample bis_WT.tab.gz,WT --sample bis_cmt23.tab.gz,cmt23 --outdir MethOneRegion --prefix chr5_19497000-19499600 --context CHG

## 1) ${PWD}:/data: means mount the current directory to /data in Docker image
## 2) bc1743f3418f: IMAGE ID (run `docker image ls` to get the IMAGE ID). 

Singularity

Build singularity image file

singularity pull docker://xie186/viewbs

This step will generate a file named viewbs.simg

Run ViewBS

• --bind: mount the current directory to /mnt

• --pwd: set initial working directory for payload process inside the container

singularity exec --bind $PWD:/mnt/ --pwd /mnt ../../viewbs.simg ViewBS  MethOneRegion --region chr5:19497000-19499600 --sample bis_WT.tab.gz,WT --sample bis_cmt23.tab.gz,cmt23 --outdir MethOneRegion --prefix chr5_19497000-19499600 --context CHG