singularity.def

Bootstrap: docker
From: ubuntu:22.04

%labels
    Author Nick Youngblut
    Version 1.0
    Description STATE - machine learning model for cellular perturbation prediction
    
%help
    This container includes STATE (https://github.com/ArcInstitute/state), a machine learning model
    that predicts cellular perturbation response across diverse contexts.
    
    STATE is trained on single-cell RNA-seq data and can predict how cells respond to various
    perturbations including drugs, genetic modifications, and environmental changes.

    To build with singularity, run:
        singularity build state.sif singularity.def

    To run the container, run:
        singularity run state.sif --help

%environment
    export PATH="/root/.local/bin:$PATH"
    
%post
    # Install system dependencies
    apt-get update && apt-get install -y \
        curl \
        build-essential \
        python3-dev \
        && rm -rf /var/lib/apt/lists/*
    
    # Install uv
    curl -LsSf https://astral.sh/uv/install.sh | sh
    
    # Install STATE
    /root/.local/bin/uv tool install arc-state

%runscript
    exec state "$@"