sv_calling_docker

This repository contains a dockerfile and build script to make a container for SV calling from WG(B)S

Why a Docker container?

The main goal of building this container is simplify the dependency requirements to jointly call SVs from WGS and WGBS using either BWA or BISCUIT, respectively.

BISCUIT: https://github.com/huishenlab/biscuit

bwa: http://bio-bwa.sourceforge.net/

Building a new container

To build a container, you need to have Docker installed (which requires one to have root access)

1. Clone the repo:

git clone https://github.com/huishenlab/sv_calling_docker.git

Modify and document version changes to software if needed in the Dockerfile or docker-build.sh. Ideally, documenting any changes should be done in the NEWS.md since it is effectively a new release.

(Re)build the container:

docker build --no-cache -t varishenlab:sv_calling .

Push it onto dockerhub:

1. Generate an access token from the varishenlab dockerhub.

2. Login to docker using the access token:

docker login --username varishenlab

3. You'll now be prompted for a password:

Password: your_access_token_goes_here

4. Now tag and push it:

# Tag the release
docker tag varishenlab:sv_calling varishenlab/sv_calling:sv_calling

# Push
docker push varishenlab/sv_calling:sv_calling

Pull the container via singularity

To use the container on HPC, which doesn't have a Docker daemon running, you will need to pull and build the .sif file using singularity.

# Load the singularity module
# Note this is currently (2020-01-7) not needed
# module load singularity

# Pull the docker image and generate a SIF file
singularity pull docker://varishenlab/sv_calling:sv_calling

# Rename because the repo name gets appended
mv sv_calling_sv_calling.sif sv_calling.sif

Pull the container using Docker

# Pull the docker image
docker pull varishenlab/sv_calling:sv_calling

Logging into the container to see where things are

# Using singularity
singularity shell sv_calling.sif

# Using docker
docker run -it varishenlab:sv_calling /bin/bash