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Containerized Installation

Downloading Required Databases and Software

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 -r requirements.txt

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

wget https://raw.githubusercontent.com/mrueda/cbicall/refs/heads/main/scripts/01_download_external_data.py
python3 ./01_download_external_data.py

Note: Google Drive can be a tad restrictive with the download. If you get an error, please use the error URL link in a browser and you should be able to retrieve it there.

Once downloaded, perform a checksum to make sure the files were not corrupted:

md5sum -c data.tar.gz.md5

Now let's reassemble the split files into the original tar archive:

cat data.tar.gz.part-?? > data.tar.gz

Clean up split files to save space (when you think you are ready!):

rm data.tar.gz.part-??

Extract the tar archive:

tar -xzvf data.tar.gz

Finally, in the cbicall repo:

Change DATADIR variable in workflows/bash/*/parameters.sh and workflows/snakemake/*/config.yaml so that it matches the location of your downloaded data.

Method 2: 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 3: 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 -t cnag/cbicall:latest .
  • For Docker versions older than 19.03 (no buildx support):
docker build -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

To connect to the container:

docker exec -ti cbicall bash

Finally, inside the cbicall repo:

Change DATADIR variable in workflows/bash/parameters.sh and workflows/snakemake/config.yaml to /cbicall-data.

Performing unit test

Inside the container

cd examples/input
./run_test.sh

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 (untested).
  • 16GB of RAM
  • >= 1 core (ideally i7 or Xeon).
  • At least 100GB HDD.

Common errors: Symptoms and treatment

  • Dockerfile:
      * DNS errors

    - Error: Temporary failure resolving 'foo'

      Solution: https://askubuntu.com/questions/91543/apt-get-update-fails-to-fetch-files-temporary-failure-resolving-error