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Phase 2: AF3 execution, job monitoring, Mol* viewer, progress notes
- Added run_af3.py: sbatch script generation for gpu-micro.q - Added check_job_status.py: monitor SLURM jobs via sacct - Added check_completion.yml: cron workflow (every 15min) - Added end_competition.yml: manual trigger to publish all results - Added end_competition.py: generate public gallery - Added setup_runner.sh: self-hosted runner installation - Added templates/viewer.html: Mol* with pLDDT coloring - Added PROGRESS.md: session notes + GitHub Classroom plan - Updated prepare_af3_input.py: correct AF3 format (dialect, version, id) - Updated process_submission.yml: save status.json with job tracking
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‎.github/workflows/check_completion.yml‎

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name: Check Job Completion
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on:
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# Run every 15 minutes
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schedule:
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- cron: '*/15 * * * *'
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# Allow manual trigger
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workflow_dispatch:
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jobs:
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check-jobs:
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runs-on: [self-hosted, af3-runner]
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permissions:
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issues: write
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contents: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Find processing submissions
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id: find
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run: |
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# Find all submissions with processing status
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PROCESSING_DIRS=""
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for dir in results/submission_*; do
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if [ -d "$dir" ]; then
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STATUS_FILE="$dir/status.json"
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if [ -f "$STATUS_FILE" ]; then
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STATUS=$(python3 -c "import json; print(json.load(open('$STATUS_FILE')).get('status', 'unknown'))" 2>/dev/null || echo "unknown")
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if [ "$STATUS" = "processing" ] || [ "$STATUS" = "submitted" ]; then
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PROCESSING_DIRS="$PROCESSING_DIRS $dir"
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fi
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fi
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fi
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done
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echo "dirs=$PROCESSING_DIRS" >> $GITHUB_OUTPUT
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- name: Check each job
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if: steps.find.outputs.dirs != ''
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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RESULTS_URL: ${{ vars.RESULTS_URL || 'https://YOUR_GITHUB_PAGES_URL/results' }}
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run: |
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for dir in ${{ steps.find.outputs.dirs }}; do
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echo "Checking $dir..."
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# Read status file
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STATUS_FILE="$dir/status.json"
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if [ ! -f "$STATUS_FILE" ]; then
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continue
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fi
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JOB_ID=$(python3 -c "import json; print(json.load(open('$STATUS_FILE')).get('slurm_job_id', ''))" 2>/dev/null)
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ISSUE_NUM=$(python3 -c "import json; print(json.load(open('$STATUS_FILE')).get('issue_number', ''))" 2>/dev/null)
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if [ -z "$JOB_ID" ] || [ -z "$ISSUE_NUM" ]; then
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echo "Missing job_id or issue_number in $STATUS_FILE"
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continue
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fi
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# Check job status
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python3 scripts/check_job_status.py \
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--submission-dir "$dir" \
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--job-id "$JOB_ID" \
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--results-dir "public_results" \
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--output-format json > job_result.json 2>&1 || true
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COMPLETED=$(python3 -c "import json; print(json.load(open('job_result.json')).get('completed', False))")
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SUCCESS=$(python3 -c "import json; print(json.load(open('job_result.json')).get('success', False))")
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TOKEN=$(python3 -c "import json; print(json.load(open('job_result.json')).get('result_token', '') or '')")
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if [ "$COMPLETED" = "True" ]; then
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if [ "$SUCCESS" = "True" ] && [ -n "$TOKEN" ]; then
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# Success - notify participant with private link
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VIEWER_URL="${RESULTS_URL}/../viewer.html?token=${TOKEN}"
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gh issue comment "$ISSUE_NUM" --body "## Results Ready
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Your AlphaFold3 prediction has completed successfully.
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**View your structure:** [Open in Mol* Viewer](${VIEWER_URL})
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**Download files:**
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- [Structure (CIF)](${RESULTS_URL}/${TOKEN}/)
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> Note: This link is unique to your submission. Please save it for your records.
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Results will remain private until the competition ends."
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gh issue edit "$ISSUE_NUM" --remove-label "processing" --add-label "completed"
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else
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# Failed
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ERROR=$(python3 -c "import json; print(json.load(open('job_result.json')).get('error', 'Unknown error'))")
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gh issue comment "$ISSUE_NUM" --body "## Prediction Failed
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Unfortunately, your AlphaFold3 prediction encountered an error:
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\`\`\`
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${ERROR}
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\`\`\`
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Please check your sequence and try submitting again. Common issues:
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- Sequence too long (>5000 residues)
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- Invalid amino acid characters
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- Server resource limitations
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If the problem persists, please contact the organizers."
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gh issue edit "$ISSUE_NUM" --remove-label "processing" --add-label "failed"
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fi
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fi
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rm -f job_result.json
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done
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- name: Commit status updates
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run: |
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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git add -A results/ public_results/ || true
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git diff --staged --quiet || git commit -m "Update job statuses [skip ci]"
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git push || true

‎.github/workflows/end_competition.yml‎

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name: End Competition
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on:
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workflow_dispatch:
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inputs:
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confirm:
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description: 'Type "END" to confirm ending the competition'
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required: true
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type: string
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jobs:
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end-competition:
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if: github.event.inputs.confirm == 'END'
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runs-on: [self-hosted, af3-runner]
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permissions:
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contents: write
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pages: write
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issues: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Publish all results
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run: |
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python3 scripts/end_competition.py \
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--results-dir results \
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--public-dir docs \
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--results-url results
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- name: Update all issues
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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# Get all issues with 'submission' label
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gh issue list --label submission --state all --json number,title --limit 1000 | \
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python3 -c "
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import json, sys
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issues = json.load(sys.stdin)
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for issue in issues:
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print(issue['number'])
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" | while read ISSUE_NUM; do
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gh issue comment "$ISSUE_NUM" --body "## Competition Ended
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The protein design competition has concluded. All results are now public.
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View the final results and all submissions at the competition gallery:
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**[View All Results](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/)**
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Thank you for participating!"
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gh issue edit "$ISSUE_NUM" --add-label "competition-ended"
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done
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- name: Commit and push
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run: |
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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git add docs/
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git commit -m "End competition - publish all results"
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git push
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- name: Summary
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run: |
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echo "## Competition Ended" >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "All results have been published to GitHub Pages." >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "View at: https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/" >> $GITHUB_STEP_SUMMARY

‎.github/workflows/process_submission.yml‎

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types: [labeled]
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jobs:
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validate-and-prepare:
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validate-and-run:
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if: github.event.label.name == 'submission'
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runs-on: [self-hosted, af3-runner]
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Create submission directory
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run: |
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SUBMISSION_ID="submission_${{ github.event.issue.number }}"
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ISSUE_BODY: ${{ github.event.issue.body }}
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ISSUE_NUMBER: ${{ github.event.issue.number }}
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run: |
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python scripts/parse_submission.py \
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python3 scripts/parse_submission.py \
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--issue-body "$ISSUE_BODY" \
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--issue-number "$ISSUE_NUMBER" \
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--output-dir "$SUBMISSION_DIR"
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- name: Prepare AF3 input
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id: prepare
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run: |
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python scripts/prepare_af3_input.py \
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python3 scripts/prepare_af3_input.py \
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--submission-dir "$SUBMISSION_DIR" \
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--submission-id "$SUBMISSION_ID"
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- name: Submit AF3 job to SLURM
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id: submit
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run: |
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python3 scripts/run_af3.py \
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--submission-dir "$SUBMISSION_DIR" \
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--submission-id "$SUBMISSION_ID" \
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--mode full \
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--submit 2>&1 | tee submit_output.txt
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# Extract job ID from sbatch output
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JOB_ID=$(grep -oP 'Submitted batch job \K\d+' submit_output.txt || echo "unknown")
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echo "SLURM_JOB_ID=${JOB_ID}" >> $GITHUB_ENV
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# Save status file for tracking
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cat > "$SUBMISSION_DIR/status.json" << EOF
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{
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"status": "processing",
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"slurm_job_id": "${JOB_ID}",
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"issue_number": ${{ github.event.issue.number }},
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"submitted_at": "$(date -Iseconds)"
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}
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EOF
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- name: Comment on success
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if: success()
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uses: actions/github-script@v7
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issue_number: context.issue.number,
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owner: context.repo.owner,
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repo: context.repo.repo,
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body: `## Submission Received\n\nYour sequence has been validated and queued for AlphaFold3 processing.\n\n**Submission ID:** \`${{ env.SUBMISSION_ID }}\`\n\nYou will receive your results privately once processing is complete.`
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body: `## Submission Received\n\nYour sequence has been validated and submitted to AlphaFold3.\n\n**Submission ID:** \`${{ env.SUBMISSION_ID }}\`\n**SLURM Job ID:** \`${{ env.SLURM_JOB_ID }}\`\n\nYou will receive your results privately once processing is complete.`
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})
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github.rest.issues.addLabels({
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issue_number: context.issue.number,
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owner: context.repo.owner,
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repo: context.repo.repo,
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labels: ['processing']
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})
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- name: Comment on failure

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