README.quay.md

MetaPathways

MetaPathways is a pipeline for processing and annotating assembled metagenomic sequences.

• Source and documentation: https://github.com/hallamlab/MetaPathways
• Releases and Apptainer downloads: https://github.com/hallamlab/MetaPathways/releases
• Issues: https://github.com/hallamlab/MetaPathways/issues
• License: MIT
• Platform: Linux x86-64 (amd64), Python 3.11

Release containers contain the validated MetaPathways Conda package and its pinned dependency versions. They include the core annotation pipeline; optional MAGSplitter, camelot-frs, and licensed Pathway Tools require separate installation.

Docker

Use a version tag for reproducible work (replace VERSION with a published release, such as 3.5.0):

docker pull quay.io/hallamlab/metapathways:VERSION
docker run --rm quay.io/hallamlab/metapathways:VERSION metapathways version
docker run --rm -v "$PWD:/work" -w /work --user "$(id -u):$(id -g)" quay.io/hallamlab/metapathways:VERSION metapathways run --help

Mount your input files, configuration, reference databases, and output directory when running a pipeline. The latest tag tracks stable releases; release candidates do not update it.

Apptainer / Singularity

Download the .sif file and container checksums from the corresponding GitHub release, or convert the Docker image:

apptainer pull metapathways.sif docker://quay.io/hallamlab/metapathways:VERSION
apptainer exec metapathways.sif metapathways version
apptainer exec --bind "$PWD:/work" --pwd /work metapathways.sif metapathways run --help

The image contains software, not production reference databases. Follow the source repository's documentation to configure your data and databases.