963215de2d
- Add filter to skip .zip and .tar.gz files when creating result archive - Update CRISPR feature with CASFinder dependencies (hmmer, blast, vmatch, etc.) - Add install-casfinder task for macsydata installation - Remove obsolete CRISPR test files Co-Authored-By: Claude <noreply@anthropic.com>
92 lines
2.4 KiB
Bash
92 lines
2.4 KiB
Bash
#!/bin/bash
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# Entrypoint script for bttoxin-pipeline
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# Activates pixi environment and starts services
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set -e
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# Create jobs directory
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mkdir -p /app/jobs
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# Install nginx from apt if not already installed
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if ! command -v nginx &> /dev/null; then
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echo "Installing nginx..."
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apt-get update > /dev/null 2>&1
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DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends nginx curl > /dev/null 2>&1
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rm -rf /var/lib/apt/lists/*
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fi
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# Create shell-hook script for webbackend environment (includes uvicorn)
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echo "Activating pixi webbackend environment..."
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pixi shell-hook -e webbackend > /app/activate.sh
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echo 'exec "$@"' >> /app/activate.sh
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# Create nginx config in /tmp (writable)
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cat > /tmp/nginx.conf << 'NGINXCONF'
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worker_processes auto;
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pid /tmp/nginx.pid;
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error_log /tmp/nginx_error.log;
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events {
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worker_connections 1024;
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}
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http {
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include /etc/nginx/mime.types;
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default_type application/octet-stream;
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log_format main '$remote_addr - $remote_user [$time_local] "$request" '
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'$status $body_bytes_sent "$http_referer" '
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'"$http_user_agent"';
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access_log /tmp/nginx_access.log main;
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sendfile on;
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keepalive_timeout 65;
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client_max_body_size 100M;
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server {
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listen 80;
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server_name _;
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root /var/www/html;
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index index.html;
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gzip on;
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gzip_types text/plain text/css application/json application/javascript;
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location / {
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try_files $uri $uri/ /index.html;
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}
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location /api/ {
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proxy_pass http://127.0.0.1:8000/api/;
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proxy_http_version 1.1;
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proxy_set_header Host $host;
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proxy_set_header X-Real-IP $remote_addr;
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proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
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proxy_set_header X-Forwarded-Proto $scheme;
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}
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location = /health {
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proxy_pass http://127.0.0.1:8000/api/health;
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}
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}
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}
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NGINXCONF
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# Start services using the shell hook
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echo "Starting BtToxin Pipeline services..."
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exec /bin/bash /app/activate.sh bash -c "
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mkdir -p /app/jobs
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# Set API_BASE_URL from environment or default
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export API_BASE_URL=\${API_BASE_URL:-http://localhost}
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# Start nginx with custom config
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nginx -c /tmp/nginx.conf &
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# Start backend
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uvicorn backend.app.main:app --host 127.0.0.1 --port 8000 &
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wait
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"
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