Dockerfile2

# Must be built *after* the main Dockerfile in this repo (docker build -f
# Dockerfile -t funannotate:latest .) -- the public nextgenusfs/funannotate
# image does not have the Rust-optimized PASA/EVM engine this repo builds.
FROM funannotate:latest

# Install FUNANNOTATE_DB with all lineage databases
# This layer can be large (~5-10GB), so it's separate for caching efficiency
RUN mkdir -p /opt/databases && \
    funannotate setup -i all --wget -b dikarya microsporidia embryophyta metazoa arthropoda vertebrata protists tetrapoda -d /opt/databases

# Verify database installation
RUN funannotate database -d /opt/databases --show-versions 2>/dev/null || echo "Databases installed"

# Set environment variable
ENV FUNANNOTATE_DB="/opt/databases"

SHELL ["/bin/bash", "-c"]
CMD ["funannotate", "--help"]