128 lines
4.5 KiB
Plaintext
128 lines
4.5 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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// Pipeline parameters
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params.pdb = 's3://omic/eureka/Pocketminer/1HSG.pdb'
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params.outdir = 's3://omic/eureka/Pocketminer/output'
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params.model_path = '/workspace/gvp/models/pocketminer'
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params.debug = false
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process POCKETMINER {
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container 'harbor.cluster.omic.ai/omic/pocketminer:latest'
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publishDir params.outdir, mode: 'copy'
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input:
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val pdb_path
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output:
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path "*-preds.npy", emit: predictions_npy
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path "*-predictions.txt", emit: predictions_txt
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path "*-summary.json", emit: summary
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path "*_X.npy", optional: true, emit: features_debug
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path "*_S.npy", optional: true, emit: sequence_debug
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path "*_mask.npy", optional: true, emit: mask_debug
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path "run.log", emit: log
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script:
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def debug_flag = params.debug ? '--debug' : ''
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"""
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set +e
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touch run.log
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echo "=== Environment Debug ===" >> run.log
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echo "Input path: ${pdb_path}" >> run.log
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echo "AWS_ENDPOINT_URL: \${AWS_ENDPOINT_URL:-not set}" >> run.log
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echo "AWS_ACCESS_KEY_ID set: \${AWS_ACCESS_KEY_ID:+yes}" >> run.log
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ls /omic/eureka/ >> run.log 2>&1 || echo "/omic/eureka not mounted" >> run.log
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echo "=== End Debug ===" >> run.log
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PDB_FILE=""
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# Method 1: Direct path (if PVC mounted or local)
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if [ -f "${pdb_path}" ]; then
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echo "Found at direct path" >> run.log
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cp "${pdb_path}" input.pdb && PDB_FILE="input.pdb"
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fi
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# Method 2: Convert s3://omic/... to /omic/... (PVC mount path)
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if [ -z "\$PDB_FILE" ]; then
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PVC_PATH="\$(echo '${pdb_path}' | sed 's|^s3://|/|')"
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if [ -f "\$PVC_PATH" ]; then
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echo "Found at PVC path: \$PVC_PATH" >> run.log
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cp "\$PVC_PATH" input.pdb && PDB_FILE="input.pdb"
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else
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echo "Not found at PVC path: \$PVC_PATH" >> run.log
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fi
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fi
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# Method 3: Download from MinIO using python
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if [ -z "\$PDB_FILE" ]; then
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S3_PATH="${pdb_path}"
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ENDPOINT="\${AWS_ENDPOINT_URL:-http://datalake-hl.datalake.svc.cluster.local:9000}"
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echo "Downloading via python S3 from: \$ENDPOINT" >> run.log
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echo "S3 path: \$S3_PATH" >> run.log
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echo "AWS_ACCESS_KEY_ID: \${AWS_ACCESS_KEY_ID:+set}" >> run.log
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echo "AWS_SECRET_ACCESS_KEY: \${AWS_SECRET_ACCESS_KEY:+set}" >> run.log
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echo "AWS_ENDPOINT_URL: \${AWS_ENDPOINT_URL:-not set}" >> run.log
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# Install boto3 if needed, then download
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pip install -q boto3 2>> run.log || conda install -y -q boto3 2>> run.log || true
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python -c "
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import os, sys
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s3_path = os.environ.get('S3_INPUT', '${pdb_path}')
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endpoint = os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000')
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path = s3_path.replace('s3://', '')
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parts = path.split('/', 1)
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bucket, key = parts[0], parts[1]
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print(f'Bucket: {bucket}, Key: {key}, Endpoint: {endpoint}')
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import boto3
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from botocore.client import Config
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s3 = boto3.client('s3',
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endpoint_url=endpoint,
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aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', ''),
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aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', ''),
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config=Config(signature_version='s3v4'),
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region_name='us-east-1'
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)
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s3.download_file(bucket, key, 'input.pdb')
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size = os.path.getsize('input.pdb')
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print(f'Downloaded {size} bytes')
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" >> run.log 2>&1
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if [ -f input.pdb ] && [ -s input.pdb ]; then
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echo "S3 download successful (\$(wc -c < input.pdb) bytes)" >> run.log
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PDB_FILE="input.pdb"
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else
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echo "S3 download failed - check run.log" >> run.log
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cat run.log
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rm -f input.pdb
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fi
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fi
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set -e
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if [ -z "\$PDB_FILE" ] || [ ! -f input.pdb ]; then
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echo "ERROR: Could not retrieve PDB file from any source" >> run.log
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cat run.log
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exit 1
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fi
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echo "PDB file ready (\$(wc -c < input.pdb) bytes)" >> run.log
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PDB_BASENAME="\$(basename '${pdb_path}' .pdb)"
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python /workspace/entrypoint.py \\
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--pdb input.pdb \\
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--output-folder . \\
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--output-name "\$PDB_BASENAME" \\
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--model-path ${params.model_path} \\
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${debug_flag} 2>&1 | tee -a run.log
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echo "Pipeline completed successfully" >> run.log
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"""
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}
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workflow {
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POCKETMINER(params.pdb)
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}
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