/setup-cron

You are helping set up a cron job to automatically monitor and progress VGP workflows.

Your Task

1. Understand the environment:

   • Ask user about their environment (local, HPC, SLURM)
   • Ask about preferred polling interval (hourly recommended)
   • Ask if they want automatic retry of failed workflows
   • Determine log file location preference

2. Verify manual command works:

   cd /path/to/VGP-planemo-scripts
   vgp-run-all --resume -p profile.yaml -m ./metadata/ --quiet
   

   Confirm this runs successfully before proceeding.

3. Create wrapper script if needed (especially for HPC):

   #!/bin/bash
   # ~/vgp_cron.sh
   source ~/.bashrc
   cd /path/to/VGP-planemo-scripts || exit 1
   vgp-run-all --resume -p profile.yaml -m ./metadata/ --quiet 2>&1
   

   Make it executable: chmod +x ~/vgp_cron.sh

4. Generate cron entry based on preferences:

   Basic hourly (recommended):

   0 * * * * cd /path/to/VGP-planemo-scripts && vgp-run-all --resume -p profile.yaml -m ./metadata/ --quiet >> cron.log 2>&1
   

   Every 30 minutes:

   0,30 * * * * cd /path/to/VGP-planemo-scripts && vgp-run-all --resume -p profile.yaml -m ./metadata/ --quiet >> cron.log 2>&1
   

   With automatic retry:

   0 * * * * cd /path/to/VGP-planemo-scripts && vgp-run-all --resume --retry-failed -p profile.yaml -m ./metadata/ --quiet >> cron.log 2>&1
   

   HPC with wrapper script:

   0 * * * * /home/user/vgp_cron.sh >> /home/user/vgp_cron.log 2>&1
   

5. Provide setup instructions:

   # Edit crontab
   crontab -e
   
   # Add the cron entry (paste the line from above)
   
   # Verify it's added
   crontab -l
   

6. Show monitoring commands:

   # Watch logs in real-time
   tail -f cron.log
   
   # Check recent activity
   tail -50 cron.log
   
   # Search for errors
   grep -i "error\|fail" cron.log
   

7. Provide troubleshooting tips:

   • Environment variables: Use source ~/.bashrc
   • Working directory: Always include cd /path
   • Absolute paths: Never use relative paths in cron
   • Test manually first: Run exact command before adding to cron
   • Log redirection: Always use >> log.txt 2>&1

Output Format

Provide:

1. ✅ Prerequisites checklist
2. 📝 Recommended cron entry (copy-paste ready)
3. 🔧 Setup commands
4. 👀 Monitoring commands
5. 🐛 Troubleshooting tips