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Build

Set Up Build Environment

The best way to build is set up an AWS EC2 instance and build the docker containers from there. Building from your local machine is definitely possible, but you will probably hear heavy CPU fan noise (and possibly some smoke).

Prerequisites:

  • Miniconda
  • Docker
  • bash, curl, wget, tar, git
conda create -n scing python=3.8 pip
conda activate scing
conda install -c cyclus java-jre
git clone https://github.com/hisplan/scing.git
pip install .

Configure

Set registry in config.yaml to your container registry.

The following will use, for example, hisplan in Docker Hub as your container registry. Replace hisplan with yours.

versoin: 1.0
containers:
  registry: docker.io/hisplan

If you want to use Red Hat Quay.io:

versoin: 1.0
containers:
  registry: quay.io/dpeerlab

where dpeerlab should be replaced with your own Quay.io namespace.

If you want to use Amazon ECR (EC2 Container Registry):

versoin: 1.0
containers:
  registry: 583643567512.dkr.ecr.us-east-1.amazonaws.com

where 583643567512.dkr.ecr.us-east-1.amazonaws.com should be replaced with your own AWS ECR.

Log In to Your Container Registry

Docker Hub

docker login

Red Hat Quay.io

docker login quay.io

In addition to the login, you must set an OAuth access token so that the build script can create public repositories in Red Hat Quay.io:

export QUAY_AUTH_TOKEN="xyz-123-abc"

If you don't have one, you can create one by following this instruction.

Amazon ECR

aws ecr get-login-password --region us-east-1 | docker login --username AWS --password-stdin 583643567512.dkr.ecr.us-east-1.amazonaws.com

where 583643567512.dkr.ecr.us-east-1.amazonaws.com is your registry address.

Build

In case some of the GitHub repositories are in private mode, you must set up GitHub auth token to access those private repositories. If you want to use your GitHub auth token to access all the repositories specified in the config file, you can set up the environment variable as shown below:

export GIT_AUTH_TOKEN="abc-123-xyz"

If only some of the repositories are private or if you need to specify different GitHub auth tokens for different repositoires, then you can set up auth token on a per-image basis as shown below:

- name: cellranger-atac
  version: 2.0.0
  project_url: https://github.com/hisplan/docker-cellranger-atac
  download_url: https://github.com/hisplan/docker-cellranger-atac/archive/refs/tags/v2.0.0.tar.gz
  git_auth_token: abc-123-xyz

If everything is publicly available, you don't need to worry about GitHub auth token.

During the build process, 10x software (e.g. Cell Ranger) will be dockerized. To do this, you must first sign the 10x Genomics End User Software License Agreement (EULA). To automate the build process (e.g. CI/CD), make sure you sign the 10x Genomics EULA first:

scing download \
  --site-url="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/6.0/" \
  --agree-eula

Run the build script:

scing build --config=config.yaml

Job File

When you create a job file (e.g. a job file for scATAC-seq), make sure you set the dockerRegistry parameter to your own docker registry:

{
    "CellRangerATAC.sampleName": "test_sample1",
    "CellRangerATAC.fastqNames": "test_sample1",
    "CellRangerATAC.fastqFiles": [
        "s3://.../test_sample1_L001_I1_001.fastq.gz",
        "s3://.../test_sample1_L001_R1_001.fastq.gz",
        "s3://.../test_sample1_L001_R2_001.fastq.gz",
        "s3://.../test_sample1_L001_R3_001.fastq.gz",
    ],
    "CellRangerATAC.referenceGenome": {
        "name": "GRCh38-2020-A-2.0.0",
        "location": "https://cf.10xgenomics.com/supp/cell-atac/refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz"
    },
    "CellRangerATAC.dockerRegistry": "${YOUR_DOCKER_REGISTRY}"
}