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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

1. Install Nextflow

# via the official installer
curl -s https://get.nextflow.io | bash
mv nextflow ~/.local/bin/

# verify
nextflow -version

Or with Conda/Mamba:

mamba create -n nf nextflow
conda activate nf

2. Install a container engine

Follow the Docker installation guide. Verify with docker --version.

Follow the Apptainer installation guide. Verify with apptainer --version.

Install Miniconda or Mamba. All tool environments are managed per-process by Nextflow.

3. antiSMASH database

The pipeline can download the database automatically on first run. To pre-download it manually:

# pull the antiSMASH container and run the download helper
docker pull antismash/standalone:8.0.4
docker run --rm -v /path/to/db:/db \
    antismash/standalone:8.0.4 \
    antismash-download-databases /db

# create an antiSMASH environment and run the download helper
conda create -n antismash -c conda-forge -c bioconda antismash=8
conda activate antismash
antismash-download-databases

Pass the database path to the pipeline with --antismash_db /path/to/db. If the path is absent or empty, the pipeline downloads the database there automatically before running antiSMASH.

deepBGC model data is also downloaded automatically on first run unless --deepbgc_data_dir points to an existing directory. Ensure outbound network access for the initial deepBGC run.

4. Clone the repository (optional)

Running nextflow run exterex/clystere pulls the pipeline automatically from GitHub. To work with a local copy:

git clone https://github.com/exterex/clystere.git
cd clystere
nextflow run . --input samplesheet.csv --outdir results -profile docker