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Non-containerized Installation

Use this path if you want to run beacon2-cbi-tools directly on the host without Docker or Apptainer.

1. Prepare external data

Work in a directory with at least 150 GB of free space:

wget https://raw.githubusercontent.com/CNAG-Biomedical-Informatics/beacon2-cbi-tools/main/deploy/01_download_external_data.py
python3 01_download_external_data.py
md5sum -c data.tar.gz.md5
cat data.tar.gz.part-?? > data.tar.gz
tar -xzvf data.tar.gz
mkdir tmp

If Google Drive blocks the download, use the URL printed by the script and fetch the file manually.

Then edit:

/path/to/downloaded/data/soft/NGSutils/snpEff_v5.0/snpEff.config

Set:

data.dir = /path/to/downloaded/data/soft/NGSutils/snpEff_v5.0/data

2. Install system packages

sudo apt install git wget gcc make libperl-dev libbz2-dev zlib1g-dev libncurses5-dev libncursesw5-dev liblzma-dev libcurl4-openssl-dev libssl-dev cpanminus perl python3 python3-pip default-jre

If you plan to use MongoDB loading, install mongosh as well.

3. Clone the repository

git clone https://github.com/CNAG-Biomedical-Informatics/beacon2-cbi-tools.git
cd beacon2-cbi-tools

To update an existing checkout later:

git pull

4. Install Python and Perl dependencies

Core Python dependencies:

pip install -r requirements.txt

Core Perl dependencies:

cpanm --notest --installdeps .

Optional utility dependencies:

pip install -r utils/bff_browser/requirements.txt
cpanm --notest Mojolicious MongoDB Minion Minion::Backend::SQLite

Documentation site dependencies are managed separately under docs-site/ with Node.js and npm.

5. Configure the toolkit

Update bin/config.yaml so that:

  • base points to the directory where you unpacked the external data
  • mongosh points to the correct executable on your system

6. Test the deployment

cd deploy
bash 02_test_deployment.sh

Installing jq may help when running the test scripts.

System requirements

  • linux/amd64 or linux/arm64
  • Python 3.8+
  • Perl 5
  • at least 4 GB RAM, ideally more
  • at least 200 GB of disk space for the full data setup

Troubleshooting

If Python modules are missing, rerun:

pip install -r requirements.txt

If Perl modules are missing, rerun:

cpanm --notest --installdeps .