Workflows such as cellranger_workflow and dropseq_workflow provide the option of running
bcl2fastq. We provide dockers
bcl2fastq that are accessible only by members of the Broad Institute. Non-Broad Institute members will have to provide
their own docker images. Please note that if you’re a Broad Institute member and are not able to pull the docker image, please check
https://app.terra.bio/#groups to see that you’re a member of the all_broad_users group. If not, please contact
Terra support and ask to be added to the firstname.lastname@example.org group.
Read this tutorial if you are new to Docker.
Then for a Debian based docker (e.g. continuumio/miniconda3), create the Dockerfile as follows:
RUN apt-get update && apt-get install --no-install-recommends -y alien unzip ADD 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-v188.8.131.522-Linux-x86_64.rpm && rm /software/bcl2fastq2-v2*
bcl2fastq from the Illumina website,
which requires registration. Choose the
Linux rpm file format and download
bcl2fastq2-v2-20-0-linux-x86-64.zip to the same directory as your Dockerfile.
You can host your private docker images in the Google Container Registry.
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,
cellranger_mkfastq_docker_registryfield of cellranger_workflow inputs.