relionSingularity.def

Bootstrap: docker
From: ubuntu:22.04

%post

    # Update and install dependencies
    apt-get update && apt-get install -y \
        wget \
        build-essential \
        libpng-dev \
        cmake \
        libfftw3-dev \
        libtiff5-dev

    # Download and extract the specific version of OpenMPI
    wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz
    tar -xzf openmpi-4.1.1.tar.gz
    cd openmpi-4.1.1

    # Configure and build OpenMPI
    ./configure --prefix=/opt/openmpi
    make -j 16 all
    make install
    echo "btl = ^openib" >> /opt/openmpi/etc/openmpi-mca-params.conf
    echo "plm_rsh_agent = /bin/false" >> /opt/openmpi/etc/openmpi-mca-params.conf
    export PATH=/opt/openmpi/bin:$PATH
    export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH

    # Download RELION source code
    wget -O relion.tar.gz https://github.com/3dem/relion/archive/refs/tags/4.0.0.tar.gz
    tar -xzvf relion.tar.gz
    cd relion-4.0.0

    # Compile and install
    mkdir build
    cd build
    cmake -DCMAKE_INSTALL_PREFIX=/usr/local/relion-4.0 -DGUI=OFF -DCUDA=OFF ..
    make -j4
    make install

%environment
    export PATH=$PATH:/usr/local/relion-4.0/bin
    export PATH=/opt/openmpi/bin:$PATH
%runscript
    #!/bin/bash
    mpirun -np $1 /usr/local/relion-4.0/bin/relion_reconstruct_mpi "${@:2}"