bcl2fastq¶

License¶

Docker¶

Read this tutorial if you are new to Docker and don’t know how to write your Dockerfile.

For a Debian based docker, add the lines below into its Dockerfile to install bcl2fastq:

RUN apt-get install --no-install-recommends -y alien unzip
ADD https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-20-0-linux-x86-64.zip /software
RUN unzip -d /software/ /software/bcl2fastq2-v2-20-0-linux-x86-64.zip && alien -i /software/bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm && rm /software/bcl2fastq2-v2*

You can host your private docker images in the Google Container Registry.

Workflows¶

Workflows such as cellranger_workflow and dropseq_workflow provide the option of running bcl2fastq. We provide dockers containing bcl2fastq that are accessible only by members of the Broad Institute. Non-Broad Institute members will have to provide their own docker images.

Example¶

In this example we create a docker image for running cellranger mkfastq version 3.0.2.

Create a GCP project or reuse an existing project.
Enable the Google Container Registry

Clone the cumulus repository:

git clone https://github.com/klarman-cell-observatory/cumulus.git

Add the lines to cumulus/docker/cellranger/3.0.2/Dockerfile to include bcl2fastq (see Docker).
Ensure you have Docker installed
Download cellranger from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/3.0

Build, tag, and push the docker. Remember to replace PROJECT_ID with your GCP project id:

cd cumulus/docker/cellranger/3.0.2/
docker build -t cellranger-3.0.2 .
docker tag cellranger-3.0.2 gcr.io/PROJECT_ID/cellranger:3.0.2
gcr.io/PROJECT_ID/cellranger:3.0.2

Import cellranger_workflow workflow to your workspace (see cellranger_workflow steps), and enter your docker registry URL (in this example, "gcr.io/PROJECT_ID/") in cellranger_mkfastq_docker_registry field of cellranger_workflow inputs.