Dockerfile2

# Extends the published base image built from this repo's main Dockerfile.
# CI builds this file after the base image is pushed to Docker Hub.
FROM nextgenusfs/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 fungi 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"]