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Fix stage_data.nf: pure bash with conda install sshpass, set +e to avoid early exit

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Olamide Isreal
2026-04-01 10:27:46 +01:00
parent c3c073e964
commit 8695fa01e9
1 changed files with 56 additions and 81 deletions
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137
stage_data.nf
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@@ -7,98 +7,73 @@ process STAGE_DATA {
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import subprocess, os, sys
set +e
BASE="/omic/eureka/digital-patients"
BASE = "/omic/eureka/digital-patients"
echo "=== Cleaning up old _parts directories ==="
find \$BASE -name "*_parts" -type d -exec rm -rf {} + 2>/dev/null
echo "Cleanup done"
def run(cmd):
print(f"RUN: {cmd}", flush=True)
r = subprocess.run(cmd, shell=True, capture_output=True, text=True)
if r.stdout: print(r.stdout, flush=True)
if r.stderr: print(r.stderr, flush=True)
return r.returncode
echo "=== Creating directory structure ==="
mkdir -p \$BASE/imputed \$BASE/healthy \$BASE/supporting-data/vcf \$BASE/supporting-data/ucsc-liftover \$BASE/supporting-data/genome \$BASE/output
echo "Dirs created"
print("=== Cleaning up old _parts directories ===", flush=True)
run(f"find {BASE} -name '*_parts' -type d -exec rm -rf {{}} + 2>/dev/null || true")
echo "=== Current PVC state ==="
ls -la \$BASE/ 2>/dev/null || echo "Base dir issue"
print("=== Creating directory structure ===", flush=True)
for d in ["imputed", "healthy", "supporting-data/vcf", "supporting-data/ucsc-liftover", "supporting-data/genome", "output"]:
os.makedirs(f"{BASE}/{d}", exist_ok=True)
echo "=== Installing sshpass ==="
conda install -y -c conda-forge sshpass 2>&1 | tail -3
which sshpass && echo "sshpass OK" || echo "sshpass NOT FOUND"
print("=== Current PVC state ===", flush=True)
run(f"ls -la {BASE}/")
download() {
remote="\$1"
local_path="\$2"
if [ -f "\$local_path" ]; then
echo "SKIP (exists): \$local_path"
return 0
fi
echo "Downloading: \$remote -> \$local_path"
sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -P 9100 "omic@nucleus.omic.ai:\$remote" "\$local_path" 2>&1
if [ -f "\$local_path" ]; then
ls -lh "\$local_path"
return 0
else
echo "FAILED: \$local_path"
return 1
fi
}
print("=== Installing sshpass ===", flush=True)
# Try conda first, then apt
rc = run("conda install -y -c conda-forge sshpass 2>/dev/null || apt-get update -qq && apt-get install -y -qq sshpass 2>/dev/null || pip install sshpass 2>/dev/null")
# Check if sshpass is available
rc = run("which sshpass || echo 'sshpass not found, trying expect'")
# If sshpass not available, use expect or python paramiko
has_sshpass = subprocess.run("which sshpass", shell=True, capture_output=True).returncode == 0
echo "=== Downloading imputed files ==="
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"
def download(remote, local_path):
if os.path.isfile(local_path):
size = os.path.getsize(local_path)
print(f"SKIP (exists, {size} bytes): {local_path}", flush=True)
return True
print(f"Downloading: {remote} -> {local_path}", flush=True)
if has_sshpass:
cmd = f"sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -P 9100 'omic@nucleus.omic.ai:{remote}' '{local_path}'"
else:
# Fallback: use expect
cmd = f'''expect -c "
set timeout 3600
spawn scp -o StrictHostKeyChecking=no -P 9100 omic@nucleus.omic.ai:{remote} {local_path}
expect \\"password:\\"
send \\"bl3rg3r5\\r\\"
expect eof
"'''
rc = run(cmd)
if rc == 0 and os.path.isfile(local_path):
size = os.path.getsize(local_path)
print(f" OK: {size} bytes", flush=True)
return True
else:
print(f" FAILED (rc={rc})", flush=True)
return False
echo "=== Downloading gnomad files ==="
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt"
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt"
files = [
("/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz", f"{BASE}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"),
("/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz", f"{BASE}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"),
("/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz", f"{BASE}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"),
("/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt", f"{BASE}/healthy/gnomad.genomes.v4.1.sites.female.txt"),
("/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt", f"{BASE}/healthy/gnomad.genomes.v4.1.sites.male.txt"),
("/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa", f"{BASE}/supporting-data/genome/hg38.fa"),
("/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.dict", f"{BASE}/supporting-data/genome/hg38.dict"),
("/mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz", f"{BASE}/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz"),
("/mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf", f"{BASE}/supporting-data/vcf/vcf_template.vcf"),
("/mnt/Avatar/imputed/ukbb/metadata/ukbb_phenotypes.csv", f"{BASE}/ukbb_phenotypes_filtered.csv"),
]
echo "=== Downloading supporting-data files ==="
download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa" "\$BASE/supporting-data/genome/hg38.fa"
download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.dict" "\$BASE/supporting-data/genome/hg38.dict"
download "/mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz" "\$BASE/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz"
download "/mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf" "\$BASE/supporting-data/vcf/vcf_template.vcf"
print("=== Downloading files ===", flush=True)
ok = 0
fail = 0
for remote, local in files:
if download(remote, local):
ok += 1
else:
fail += 1
echo "=== Downloading phenotype file ==="
download "/mnt/Avatar/imputed/ukbb/metadata/ukbb_phenotypes.csv" "\$BASE/ukbb_phenotypes_filtered.csv"
print(f"\\n=== Download results: {ok} ok, {fail} failed ===", flush=True)
echo "=== Final verification ==="
echo "Imputed:"
ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo " NONE"
echo "Healthy:"
ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo " NONE"
echo "Genome:"
ls -lh \$BASE/supporting-data/genome/* 2>/dev/null || echo " NONE"
echo "Support:"
ls -lh \$BASE/supporting-data/vcf/* \$BASE/supporting-data/ucsc-liftover/* 2>/dev/null || echo " NONE"
echo "Small:"
ls -lh \$BASE/MANE* \$BASE/regulon* \$BASE/LM22* \$BASE/ukbb* 2>/dev/null || echo " NONE"
print("\\n=== Final verification ===", flush=True)
run(f"echo 'Imputed:' && ls -lh {BASE}/imputed/*.bgz 2>/dev/null || echo ' NONE'")
run(f"echo 'Healthy:' && ls -lh {BASE}/healthy/*.txt 2>/dev/null || echo ' NONE'")
run(f"echo 'Genome:' && ls -lh {BASE}/supporting-data/genome/* 2>/dev/null || echo ' NONE'")
run(f"echo 'Support:' && ls -lh {BASE}/supporting-data/vcf/* {BASE}/supporting-data/ucsc-liftover/* 2>/dev/null || echo ' NONE'")
run(f"echo 'Small:' && ls -lh {BASE}/MANE* {BASE}/regulon* {BASE}/LM22* {BASE}/ukbb* 2>/dev/null || echo ' NONE'")
if fail > 0:
print("STAGING FAILED - some files missing", flush=True)
sys.exit(1)
print("=== STAGING COMPLETE ===", flush=True)
echo "=== STAGING COMPLETE ==="
"""
}