benchmark.yml

name: Run Simple R Script on HPC via Slurm

on:
  push:
    branches:
      - feature/metamorpheus-scripts
      # - devel

jobs:
  Benchmarking-pipeline:
    runs-on: ubuntu-latest
    env:
      FDR_THRESHOLD: 0.21

    steps:
    - name: Checkout Repository
      uses: actions/checkout@v3

    - name: Set Up SSH Access
      run: |
        mkdir -p ~/.ssh
        touch ~/.ssh/id_rsa
        chmod 600 ~/.ssh/id_rsa
        echo "${{ secrets.SSH_PRIVATE_KEY_EXPLORER }}" > ~/.ssh/id_rsa
        ssh-keyscan -H login.explorer.northeastern.edu >> ~/.ssh/known_hosts || exit 1

    - name: Transfer Files to HPC
      run: |
        scp -r benchmark raina.ans@login.explorer.northeastern.edu:/projects/VitekLab/Projects/Benchmarking || exit 1

    - name: Submit Slurm Job and Capture Job ID
      id: submit_job
      run: |
        ssh raina.ans@login.explorer.northeastern.edu "cd /projects/VitekLab/Projects/Benchmarking/benchmark && sbatch config.slurm" | tee slurm_job_id.txt 
        slurm_job_id=$(grep -oP '\d+' slurm_job_id.txt) 
        echo "Slurm Job ID is $slurm_job_id"
        echo "slurm_job_id=$slurm_job_id" >> $GITHUB_ENV  

    - name: Monitor Slurm Job
      run: |
        ssh raina.ans@login.explorer.northeastern.edu "
          while squeue -j ${{ env.slurm_job_id }} | grep -q ${{ env.slurm_job_id }}; do
            echo 'Job Id : ${{ env.slurm_job_id }} is still running...'
            sleep 10
          done
          echo 'Job has completed.'
        "

    - name: Fetch Output
      run: |
        scp -O raina.ans@login.explorer.northeastern.edu:/projects/VitekLab/Projects/Benchmarking/benchmark/job_output.txt job_output.txt
        scp -O raina.ans@login.explorer.northeastern.edu:/projects/VitekLab/Projects/Benchmarking/benchmark/job_error.txt job_error.txt

    - name: Upload Output as Artifact
      uses: actions/upload-artifact@v4
      with:
        name: benchmark-output
        path: |
          job_output.txt
          job_error.txt