asm4pg

#!/bin/bash
#SBATCH --cpus-per-task=5
#SBATCH -o slurm_logs/asm4pg_slurm_log_%j.log
#SBATCH -e slurm_logs/asm4pg_slurm_log_%j.log
#SBATCH --time=80:00:00
#SBATCH -J asm4pg
#SBATCH --mem=10G
#SBATCH --ntasks=1

# Written by Lucien Piat at INRAe
# Use this script to run asm4pg on a HPC

# Verify arguments
if [ $# -lt 1 ] || [ "$1" == "help" ]; then
    echo "Use this script to run asm4pg"
    echo ""
    echo "Usage: asm4pg [dry|run|local-run|dag|rulegraph|unlock] [additional snakemake args]"
    echo "    dry - run in dry-run mode"
    echo "    run - run the workflow with SLURM"
    echo "    local-run - run the workflow localy (on a single node)"
    echo "    dag - generate the directed acyclic graph for the workflow"
    echo "    rulegraph - generate the rulegraph for the workflow"
    echo "    unlock - Unlock the directory if snakemake crashed"
    exit 1
fi
echo "Welcome to Asm4pg! Make sure .config/masterconfig.yaml is correctly edited for this run."
MEM_MB=$(free -m | awk '/^Mem:/{print $2}')
#######################
# Update line 48 with your cluster if not on cbib or genotoul
#######################
echo '🔹 Asm4pg -> Activating execution environment'
case "${SLURM_SUBMIT_HOST:-$(hostname)}" in
    **geno**)
        echo '🔹 Asm4pg -> Identified genotoul cluster'
        module purge
        module load containers/Apptainer/1.2.5     
        source activate wf_env                     
        ;;
    **bb8**)
        echo '🔹 Asm4pg -> Identified cbib cluster, use the local-run on cbib'
        module purge
        module load miniconda/3
        eval "$(conda shell.bash hook)"
        conda activate wf_env
        MEM_MB=${SLURM_MEM_PER_NODE:-204800}
        ;;
    *)
        echo '🔹 Asm4pg -> Unkown host, or local run (if not configure this file line 48)'
        ;;
esac

run_snakemake() {
    local option="$1"
    shift  # Remove the first argument, keep the rest
    local extra_args="$@"  # Collect the rest of the arguments
    echo '🔹 Asm4pg -> Starting Snakemake workflow'
    case "$option" in
        dry)
            snakemake -c $(nproc) --dry-run --rerun-incomplete $extra_args
            ;;
        touch)
            snakemake -c $(nproc) --touch $extra_args
            ;;
        dag)
            snakemake -c $(nproc) --dag $extra_args > dag.dot 
            if [ $? -eq 0 ]; then
                echo "✅ Asm4pg -> DAG has been successfully generated as dag.dot"
            else
                echo "❌ Asm4pg -> Error: Failed to generate DAG."
                exit 1
            fi
            ;;
        rulegraph)
            snakemake -c $(nproc) --rulegraph $extra_args > rulegraph.dot 
            if [ $? -eq 0 ]; then
                echo "✅ Asm4pg -> Rulegraph has been successfully generated as rulegraph.dot"
            else
                echo "❌ Asm4pg -> Error: Failed to generate Rulegraph."
                exit 1
            fi
            ;;
        unlock)
            snakemake -c $(nproc) --unlock $extra_args
            if [ $? -eq 0 ]; then
                echo "✅ Asm4pg -> Unlocked"
            else
                echo "❌ Asm4pg -> Error: Failed to Unlocked"
                exit 1
            fi
            ;;
        run)
            snakemake --workflow-profile ./.config/snakemake/profiles/slurm --rerun-incomplete $extra_args
            ;;
        local-run)
            SNG_BIND=$(pwd)
            echo "🔹 Asm4pg -> Using $MEM_MB Mb of memory"
            snakemake --use-singularity --singularity-args "-B $SNG_BIND" -j $(nproc) --rerun-incomplete --resources mem_mb=$MEM_MB $extra_args
            ;;
        *)
            echo "Invalid option: $option"
            echo "Usage: asm4pg [dry|run|local-run|dag|rulegraph|unlock] [additional snakemake args]"
            exit 1
            ;;
    esac
}

run_snakemake "$@"