Dockerfile for bcl-convert

This is a definition file for the latest version of bcl-convert.

Illumina doesnt provide builds of bcl-convert for debian based OSes so the most convenient way to use it is with a docker or singularity.

Building the Docker image

To build the Docker image, navigate to the directory containing the Dockerfile and run the following command:

# clone this repo and navigate into the main directory
docker build -t bcl-convert-docker .

Instead of building you may want to get the container from the dockerhub repo:

docker run chaetognatha/bcl-convert:latest

To run the docker image use the following:

docker run -v /local/path:/docker/path -it bcl-convert --help

If you prefer to use a Singularity container:

sudo singularity build bcl-convert.sif docker://chaetognatha/bcl-convert:latest

IMPORTANT: converting to singularity means you have to specify a place where bcl-convert can keep logs.

First time only!

mkdir -p /tmp/bcl_convert

Run like this:

singularity run -B /tmp/bcl_convert:/var/log/bcl-convert bcl-convert.sif