ViralScan/Singularity.def at main · mdmanurung/ViralScan · GitHub

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# ViralScan Singularity / Apptainer definition file
#
# Build (requires root or --fakeroot):
#   singularity build viralscan_2.7.0.sif Singularity.def
#   apptainer build viralscan_2.7.0.sif Singularity.def
#
# Run on HPC:
#   singularity exec viralscan_2.7.0.sif \
#     viralscan -t t2g.txt -i index.idx \
#               -o output/ -s1 R1.fastq.gz -s2 R2.fastq.gz
#
# The container is built FROM the same Docker image so both images stay in sync.

Bootstrap: docker
From: condaforge/miniforge3:24.3.0-0

%labels
    Author emma.vonk@hotmail.nl
    Version 2.7.0
    Description ViralScan - viral load quantification from scRNA-seq

%help
    ViralScan v2.7.0
    ----------------
    Quantify viral load from paired-end FASTQ samples using kallisto + bustools.

    Usage example:
      singularity exec viralscan_2.7.0.sif \
        viralscan -t t2g.txt -i index.idx \
                  -o output/ -s1 R1.fastq.gz -s2 R2.fastq.gz

    See 'viralscan --help' for all options.

%files
    environment.yml /opt/environment.yml
    pyproject.toml /opt/ViralScan/pyproject.toml
    README.md /opt/ViralScan/README.md
    LICENSE /opt/ViralScan/LICENSE
    src /opt/ViralScan/src

%post
    # Install mamba and create the viralscan environment
    /opt/conda/bin/mamba env create -f /opt/environment.yml
    /opt/conda/bin/mamba clean --all -f -y
    /opt/conda/envs/viralscan/bin/python -m pip install /opt/ViralScan

    # Create a convenience wrapper so the environment is always activated
    echo '#!/bin/bash' > /usr/local/bin/viralscan
    echo 'source /opt/conda/etc/profile.d/conda.sh' >> /usr/local/bin/viralscan
    echo 'conda activate viralscan' >> /usr/local/bin/viralscan
    echo 'exec /opt/conda/envs/viralscan/bin/viralscan "$@"' >> /usr/local/bin/viralscan
    chmod +x /usr/local/bin/viralscan

%environment
    export PATH="/opt/conda/envs/viralscan/bin:$PATH"
    export CONDA_DEFAULT_ENV=viralscan

%runscript
    exec /opt/conda/envs/viralscan/bin/viralscan "$@"

%test
    /opt/conda/envs/viralscan/bin/viralscan --help
    /opt/conda/envs/viralscan/bin/kallisto version
    /opt/conda/envs/viralscan/bin/bustools version
    /opt/conda/envs/viralscan/bin/STAR --version