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Docker

Containerized Installation

Downloading Required Databases and Software​

Note: this process can be lenghty.

Begin by downloading the required databases and software. Save the data outside the container; this preserves it across container restarts and lets you update the software without downloading the data again.

Install dependencies for Python 3:

pip3 install gdown

Finally, navigate to a directory where you want the databases stored and execute:

mkdir -p /absolute/path/to/cbicall-data
wget https://raw.githubusercontent.com/mrueda/cbicall/refs/heads/main/scripts/download_cbicall_bundle.py
python3 ./download_cbicall_bundle.py --outdir /absolute/path/to/cbicall-data

To verify only the catalog-to-Google-Drive bundle identity before starting the large archive download:

python3 ./download_cbicall_bundle.py \
  --outdir /absolute/path/to/cbicall-data \
  --verify-resource-id-only

Google Drive can be restrictive with large files. If the Python download stalls or fails, print the manual download list:

python3 ./download_cbicall_bundle.py \
  --outdir /absolute/path/to/cbicall-data \
  --print-manual-download

Download every listed file into /absolute/path/to/cbicall-data, then let the script continue from those files:

python3 ./download_cbicall_bundle.py \
  --outdir /absolute/path/to/cbicall-data \
  --skip-download

The script will:

  • download missing split files when possible
  • reassemble data.tar.gz
  • verify the split parts or assembled archive with data.tar.gz.md5
  • load the CBIcall resource catalog, locally or from the catalog URL
  • optionally verify a small GDrive resource identifier file such as cbicall-resource-id.json
  • rename the verified archive using the bundle identity, for example cbicall-germline-resources-v1.tar.gz
  • extract the archive into DATADIR
  • write cbicall-resource-installation.json with the installed bundle provenance

If disk space is tight and the checksum has passed, add --remove-parts to remove data.tar.gz.part-* after assembly.

CBIcall keeps the rich resource registry in resources/cbicall-resource-catalog.json. The GDrive bundle only needs a small identifier file, for example cbicall-resource-id.json containing {"resource_key": "cbicall-germline-resources-v1"}. When that identifier file is available, the registry can store its Google Drive file ID and SHA-256 so the downloader can verify that the remote bundle matches the local CBIcall catalog entry.

Point CBIcall to your resource directory​

CBIcall workflows read resource paths from Bash env.sh files and the Snakemake config.yaml. In Docker, mount your host resource directory as /cbicall-data and point CBIcall to that container path:

sed -i 's|^DATADIR=.*|DATADIR=/cbicall-data|' workflows/bash/gatk-4.6/env.sh
sed -i 's|^DATADIR=.*|DATADIR=/cbicall-data|' workflows/bash/gatk-3.5/env.sh
sed -i 's|^datadir:.*|datadir: "/cbicall-data"|' workflows/snakemake/gatk-4.6/config.yaml

Method 1: Installing from Docker Hub (fast)​

Pull the latest Docker image from Docker Hub:

docker pull manuelrueda/cbicall:latest
docker image tag manuelrueda/cbicall:latest cnag/cbicall:latest

Method 2: Installing from Dockerfile (slow)​

Download the Dockerfile from GitHub:

wget https://raw.githubusercontent.com/CNAG-Biomedical-Informatics/cbicall/main/docker/Dockerfile

Then build the container:

  • For Docker version 19.03 and above (supports buildx):

    docker buildx build --no-cache -t cnag/cbicall:latest .

  • For Docker versions older than 19.03 (no buildx support):

    docker build --no-cache -t cnag/cbicall:latest .

Running and Interacting with the Container​

# Please update '/absolute/path/to/cbicall-data' with your actual local data path
#docker run -tid --volume /absolute/path/to/cbicall-data:/cbicall-data -e USERNAME=root --name cbicall cnag/cbicall:latest

# Real example
#docker run -tid --volume /media/mrueda/4TBB/cbicall-data:/cbicall-data -e USERNAME=root --name cbicall cnag/cbicall:latest

To connect to the container:

docker exec -ti cbicall bash

Inside the container, confirm that CBIcall sees the mounted resources:

bin/cbicall validate-resources
bin/cbicall doctor -p examples/input/param.yaml

Performing integration tests​

Inside the container, from the CBIcall repository root:

WES

bin/cbicall test --wes -t 1

mtDNA

bin/cbicall test --mit -t 1

System requirements​

  • OS/ARCH supported: linux/amd64 and linux/arm64.
  • Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOS, OpenSUSE) should do as well.
  • 16GB of RAM
  • >= 1 core (ideally i7 or Xeon).
  • At least 100GB HDD.

Common errors: Symptoms and treatment​