cuda_singularity.def

Bootstrap: docker
From: nvidia/cuda:11.0.3-base-ubuntu20.04

%help
    This is a Singularity container for running a script by Mathu Malar C (Mathu.Malar@inspection.gc.ca) that processes FAST5 files and performs downstream analysis using Guppy basecalling, mapping using Minimap2, and coverage calculation using Samtools.

%labels
    Author Mathu Malar C
    Email Mathu.Malar@inspection.gc.ca

%post
    # Update and install necessary packages
    apt-get update && apt-get install -y \
        python3 \
        python3-venv \
        wget \
        curl \
        git \
        build-essential \
        zlib1g-dev \
        libbz2-dev \
        liblzma-dev \
        libcurl4-openssl-dev \
        libssl-dev \
        libncurses5-dev \
        libncursesw5-dev

    # Install Guppy
    wget --no-check-certificate https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_6.5.7_linux64.tar.gz
    tar -xzf ont-guppy_6.5.7_linux64.tar.gz -C /opt
    rm ont-guppy_6.5.7_linux64.tar.gz
    ln -s /opt/ont-guppy/bin/* /usr/local/bin/

    # Install Minimap2
    git clone https://github.com/lh3/minimap2
    cd minimap2 && make
    cp minimap2 /usr/local/bin/
    cd .. && rm -rf minimap2

    # Install Samtools
    wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
    tar -xjf samtools-1.15.1.tar.bz2
    cd samtools-1.15.1 && ./configure --prefix=/usr/local && make && make install
    cd .. && rm -rf samtools-1.15.1 samtools-1.15.1.tar.bz2

    # Set up Python virtual environment
    python3 -m venv /opt/venv
    . /opt/venv/bin/activate

    # Upgrade pip and install Python packages
    pip install --upgrade pip
    pip install csvkit

%files
    /home/olcbio/code_github/poresippr_code/poresippr_basecall_scheduler.py /usr/local/bin/poresippr_basecall_scheduler.py
    /home/olcbio/Downloads/PoreSippRDB_240509.fasta /usr/local/bin/PoreSippRDB_240509.fasta
    /home/olcbio/Downloads/240125_MC26299/test /usr/local/bin/test
    /home/olcbio/code_github/input.csv /usr/local/bin/input.csv
    /home/olcbio/code_github/metadata.csv /usr/local/bin/metadata.csv

%environment
    # Add virtual environment to PATH
    source /opt/venv/bin/activate

%runscript
    #!/bin/bash
    source /opt/venv/bin/activate
    exec python3 /usr/local/bin/poresippr_basecall_scheduler.py "$@"