Initial commit: BtToxin Pipeline project structure

docker/digger/Dockerfile

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+# BtToxin_Digger Docker 镜像
+FROM continuumio/miniconda3:4.10.3
+
+LABEL maintainer="your-email@example.com" \
+      description="BtToxin_Digger for Pipeline" \
+      version="1.0.10"
+
+ENV LANG=C.UTF-8 \
+    PATH=/opt/conda/envs/bttoxin/bin:$PATH \
+    CONDA_DEFAULT_ENV=bttoxin \
+    PYTHONUNBUFFERED=1
+
+# 配置 conda
+RUN conda config --add channels defaults && \
+    conda config --add channels bioconda && \
+    conda config --add channels conda-forge && \
+    conda config --set channel_priority flexible && \
+    conda install -n base -c conda-forge mamba -y
+
+# 安装 BtToxin_Digger
+RUN mamba install -y \
+    python=3.7.10 \
+    perl=5.26.2 && \
+    mamba install -y \
+    bttoxin_digger=1.0.10 && \
+    conda clean -afy
+
+# 安装额外工具
+RUN apt-get update && apt-get install -y \
+    curl wget jq git && \
+    rm -rf /var/lib/apt/lists/*
+
+# 创建工作目录
+RUN mkdir -p /workspace/input /workspace/output /workspace/logs
+
+WORKDIR /workspace
+
+# 复制入口脚本
+COPY entrypoint.sh /usr/local/bin/
+RUN chmod +x /usr/local/bin/entrypoint.sh
+
+HEALTHCHECK --interval=30s --timeout=10s --retries=3 \
+    CMD BtToxin_Digger --version || exit 1
+
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
+CMD ["--help"]

docker/digger/entrypoint.sh

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+#!/bin/bash
+set -e
+
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+RED='\033[0;31m'
+NC='\033[0m'
+
+log_info() {
+    echo -e "${GREEN}[INFO]${NC} $1"
+}
+
+log_warn() {
+    echo -e "${YELLOW}[WARN]${NC} $1"
+}
+
+log_error() {
+    echo -e "${RED}[ERROR]${NC} $1"
+}
+
+init() {
+    log_info "Initializing BtToxin_Digger environment..."
+
+    if ! BtToxin_Digger --version &>/dev/null; then
+        log_error "BtToxin_Digger not found!"
+        exit 1
+    fi
+
+    log_info "BtToxin_Digger $(BtToxin_Digger --version)"
+    log_info "Python $(python --version)"
+    log_info "Perl $(perl --version | head -2 | tail -1)"
+}
+
+update_db() {
+    log_info "Updating BtToxin_Digger database..."
+    if BtToxin_Digger --update-db; then
+        log_info "Database updated successfully"
+    else
+        log_warn "Database update failed, using existing database"
+    fi
+}
+
+run_analysis() {
+    log_info "Starting toxin mining analysis..."
+    log_info "Input: $INPUT_PATH"
+    log_info "Type: $SEQUENCE_TYPE"
+    log_info "Threads: $THREADS"
+
+    BtToxin_Digger \
+        --SeqPath "$INPUT_PATH" \
+        --SequenceType "$SEQUENCE_TYPE" \
+        --Scaf_suffix "$SCAF_SUFFIX" \
+        --threads "$THREADS" \
+        2>&1 | tee /workspace/logs/digger.log
+
+    if [ $? -eq 0 ]; then
+        log_info "Analysis completed successfully"
+    else
+        log_error "Analysis failed!"
+        exit 1
+    fi
+}
+
+main() {
+    INPUT_PATH="${INPUT_PATH:-/workspace/input}"
+    SEQUENCE_TYPE="${SEQUENCE_TYPE:-nucl}"
+    SCAF_SUFFIX="${SCAF_SUFFIX:-.fna}"
+    THREADS="${THREADS:-4}"
+    UPDATE_DB="${UPDATE_DB:-false}"
+
+    init
+
+    if [ "$UPDATE_DB" = "true" ]; then
+        update_db
+    fi
+
+    if [ $# -gt 0 ]; then
+        exec BtToxin_Digger "$@"
+    else
+        run_analysis
+    fi
+}
+
+main "$@"

docker/frontend/Dockerfile

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+FROM node:18-alpine as builder
+
+WORKDIR /app
+
+COPY frontend/package*.json ./
+RUN npm ci
+
+COPY frontend/ .
+RUN npm run build
+
+FROM nginx:alpine
+
+COPY --from=builder /app/dist /usr/share/nginx/html
+COPY docker/frontend/nginx.conf /etc/nginx/conf.d/default.conf
+
+EXPOSE 80
+
+CMD ["nginx", "-g", "daemon off;"]

docker/frontend/nginx.conf

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+server {
+    listen 80;
+    server_name localhost;
+    root /usr/share/nginx/html;
+    index index.html;
+
+    location / {
+        try_files $uri $uri/ /index.html;
+    }
+
+    location /api {
+        proxy_pass http://backend:8000;
+        proxy_set_header Host $host;
+        proxy_set_header X-Real-IP $remote_addr;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+    }
+
+    location /ws {
+        proxy_pass http://backend:8000;
+        proxy_http_version 1.1;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection "upgrade";
+    }
+}

docker/worker/Dockerfile

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+FROM python:3.10-slim
+
+WORKDIR /app
+
+# 安装系统依赖
+RUN apt-get update && apt-get install -y \
+    gcc \
+    curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# 安装 Docker CLI
+RUN curl -fsSL https://get.docker.com -o get-docker.sh && \
+    sh get-docker.sh && \
+    rm get-docker.sh
+
+# 复制依赖文件
+COPY backend/requirements.txt .
+
+# 安装 Python 依赖
+RUN pip install --no-cache-dir -r requirements.txt
+
+# 复制应用代码
+COPY backend/ .
+
+CMD ["celery", "-A", "app.core.celery_app", "worker", "--loglevel=info"]