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Installation

Requirements

Dependency Minimum version Notes
Nextflow 23.04.0 NXF_VER env var can pin the version
Java 11 Required by Nextflow
Container engine — One of Docker, Singularity, Apptainer, Podman, or Conda
ICEscreen — Must be installed and accessible via ICESCREEN_ROOT

1. Install Nextflow

curl -s https://get.nextflow.io | bash
# or via conda
conda install -c bioconda nextflow

Add the nextflow binary to your PATH, or move it to a location already on it.

2. Install a container engine

advena requires access to the ICEscreen software environment. The recommended approach is Docker or Singularity with the pre-built container.

# Install Docker: https://docs.docker.com/engine/install/
docker pull exterex/icescreen-nf:latest

singularity pull icescreen-nf.sif docker://exterex/icescreen-nf:latest

# Install Mamba for faster environment resolution
conda install -n base -c conda-forge mamba

3. Install ICEscreen

advena calls ICEscreen Python scripts and databases at runtime. Point the pipeline to an ICEscreen installation by setting the ICESCREEN_ROOT environment variable or the --icescreen_root parameter.

# Clone the ICEscreen repository
git clone https://github.com/ICEscreen/ICEscreen.git /opt/icescreen

# Export the root path
export ICESCREEN_ROOT=/opt/icescreen

If ICESCREEN_ROOT is not set, advena falls back to ~/repo/icescreen then /opt/icescreen. If the databases are stored separately, override the database path with --icescreen_db.

4. Run advena

nextflow run exterex/advena \
    --input samplesheet.csv \
    --outdir results \
    -profile docker

To pin a specific version:

NXF_VER=23.10.0 nextflow run exterex/advena -r 1.0.0 \
    --input samplesheet.csv \
    --outdir results \
    -profile docker