Bcl2Fastq Dockerfile

This guide is an extension of the Cumulus Team’s guide on creating and referencing your own Dockerfile to run bcl2fastq on Alexandria/Terra.


Until cumulus/dropseq_workflow snapshot 6 is released, only launch bcl2fastq from the latest version of cumulus/bcl2fastq.

  1. Register an account on Illumina and download the Linux rpm of Bcl2Fastq.
  2. Install Docker Desktop, register a Docker account, and docker login in your terminal.
  3. Open up any text editor and save your file called Dockerfile. Place bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm in the same directory as Dockerfile.
  4. The Dockerfile should contain the following chunks:
FROM continuumio/miniconda3:4.7.12
# Install Google Cloud SDK
RUN apt-get update \
    && apt-get install --no-install-recommends -y build-essential dpkg-dev gnupg lsb-release procps curl \
    && export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" \
    && echo "deb http://packages.cloud.google.com/apt $CLOUD_SDK_REPO main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list \
    && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - \
    && apt-get update && apt-get install -y google-cloud-sdk
# Bcl2Fastq: Make sure the downloaded Bcl2Fastq RPM file is in the same directory as your Dockerfile 
ADD bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm /software/
RUN apt-get update && apt-get install --no-install-recommends -y alien \
    && alien -i /software/bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm
  1. In terminal, change directory to the folder containing the Dockerfile and enter docker build -t <yourusername>/bcl2fastq: . with your Docker username inserted.
  2. If the build does not succeed, contact jgatter@mit.edu with the Dockerfile attached. Otherwise enter docker push <yourusername>/bcl2fastq: in your terminal. Make sure to make the docker image publicly accessible!
  3. Export the most recent cumulus/bcl2fastq workflow to your Terra workspace.
  4. Edit the docker_registry variable to contain your Docker username, configure other inputs, and launch the analysis!