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Installation

Requirements

  • A UNIX system. Windows users can run the pipeline under WSL.
  • Nextflow 26.04 or newer. The pipeline is written in Nextflow's strict language, which that release makes the default parser, and manifest.nextflowVersion refuses to start on anything older. Do not set NXF_SYNTAX_PARSER.
  • A container engine: Docker, Singularity/Apptainer, Podman, Shifter or Charliecloud.
  • Disk for the databases. A full setup is roughly 100 GB, most of it DRAM and VIBRANT.

Getting the pipeline

nextflow pull deng-lab/viroprofiler              # latest
nextflow pull deng-lab/viroprofiler -r v1.0.1    # a specific release

Container images are pulled on demand; there is nothing to download by hand. If you use Singularity or Apptainer, point NXF_SINGULARITY_LIBRARYDIR at a writable directory so the converted images are reused between runs.

On aarch64 (Apple silicon, AWS Graviton, NVIDIA GB10) the published images do not apply — they are amd64 only. See ARM64.md for what can be built locally and what cannot.

Building the databases

Required once per installation, and the longest part of setting up:

nextflow run deng-lab/viroprofiler -profile docker --mode setup --db /path/to/db

Every later run takes the same --db. If entries under it are symlinks pointing elsewhere, add those targets with --container_binds a,b,c — Nextflow runs the container without your home directory mounted, so nothing outside the work directory is visible unless it is bound.

Checking the installation

# Seconds, no databases: runs every process as a no-op and proves the graph wires up.
nextflow run deng-lab/viroprofiler -stub -profile test_stub

# The bundled test dataset, end to end.
nextflow run deng-lab/viroprofiler -profile docker,test --db /path/to/db

See Profiles for choosing a container engine and an execution environment.