Skip to content
Snippets Groups Projects
Select Git revision
  • bcb8cba14d4f8f335332c268b8efad5fdad522ff
  • main default protected
  • hookup-to-django
  • small-test-to-test-pipeline
  • connect-to-adex_cache_fastapi-database
  • improve_alta_algorithm
6 results

convert_alta_to_adex_cache.py

Blame
  • Code owners
    Assign users and groups as approvers for specific file changes. Learn more.
    aggregate_and_plot.sh 782 B
    #!/usr/bin/sh
    SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
    cd $SCRIPT_DIR
    TOIL_VENV_DIR="${SCRIPT_DIR}/toil_venv"
    if [ -d "toil_venv" ]; then
        echo "Activating existing virtual environment."
        source "${TOIL_VENV_DIR}/bin/activate"
    else
        echo "Creating new virtual environment for using toil"
        python3.9 -m venv $TOIL_VENV_DIR
        source "${TOIL_VENV_DIR}/bin/activate"
        pip install --upgrade pip setuptools wheel
        pip install toil[cwl] singularity
    fi
    export SINGULARITY_BIND="/project:/project"
    export TOIL_SLURM_ARGS="--exclusive"
    toil-cwl-runner "${SCRIPT_DIR}/imaging_compress_pipeline.git/aggregate_and_plot.cwl" --workdir $SCRIPT_DIR --logDebug --singularity --batchSystem slurm --batchLogsDir ./logs --jobStore ./job_store