#!/bin/bash # 生物信息学脚本工具箱 - 学校精简版 # 基于 kejilion/sh v4.5.7 裁剪，保留：1.系统信息查询 2.系统更新 3.系统清理 4.生物信息环境搭建 00.脚本更新 0.退出 # 项目仓库: https://github.com/randomNaming/bio-project-sh sh_v="1.1.0" # 脚本分发地址（服务器 nginx 站点根，更新检查/下载均走此地址） dist_base="https://bio-sh.nknpq3nl.icu" gl_hong='\033[31m' gl_lv='\033[32m' gl_huang='\033[33m' gl_bai='\033[0m' gl_kjlan='\033[96m' permission_granted="false" # 脚本更新后，从已安装的旧版本恢复许可同意状态 CheckFirstRun_true() { if grep -q '^permission_granted="true"' /usr/local/bin/k > /dev/null 2>&1; then sed -i 's/^permission_granted="false"/permission_granted="true"/' ~/kejilion.sh elif grep -q '^permission_granted="true"' ~/kejilion.sh.bak > /dev/null 2>&1; then sed -i 's/^permission_granted="false"/permission_granted="true"/' ~/kejilion.sh fi } install() { if [ $# -eq 0 ]; then echo "未提供软件包参数!" return 1 fi for package in "$@"; do if ! command -v "$package" &>/dev/null; then echo -e "${gl_kjlan}正在安装 $package...${gl_bai}" if command -v dnf &>/dev/null; then dnf -y update dnf install -y epel-release dnf install -y "$package" elif command -v yum &>/dev/null; then yum -y update yum install -y epel-release yum install -y "$package" elif command -v apt &>/dev/null; then apt update -y apt install -y "$package" elif command -v apk &>/dev/null; then apk update apk add "$package" elif command -v pacman &>/dev/null; then pacman -Syu --noconfirm pacman -S --noconfirm "$package" elif command -v zypper &>/dev/null; then zypper refresh zypper install -y "$package" elif command -v opkg &>/dev/null; then opkg update opkg install "$package" elif command -v pkg &>/dev/null; then pkg update pkg install -y "$package" else echo "未知的包管理器!" return 1 fi fi done } remove() { if [ $# -eq 0 ]; then echo "未提供软件包参数!" return 1 fi for package in "$@"; do echo -e "${gl_kjlan}正在卸载 $package...${gl_bai}" if command -v dnf &>/dev/null; then dnf remove -y "$package" elif command -v yum &>/dev/null; then yum remove -y "$package" elif command -v apt &>/dev/null; then apt purge -y "$package" elif command -v apk &>/dev/null; then apk del "$package" elif command -v pacman &>/dev/null; then pacman -Rns --noconfirm "$package" elif command -v zypper &>/dev/null; then zypper remove -y "$package" elif command -v opkg &>/dev/null; then opkg remove "$package" elif command -v pkg &>/dev/null; then pkg delete -y "$package" else echo "未知的包管理器!" return 1 fi done } # 通用 systemctl 函数，适用于各种发行版 systemctl() { local COMMAND="$1" local SERVICE_NAME="$2" if command -v apk &>/dev/null; then service "$SERVICE_NAME" "$COMMAND" else /bin/systemctl "$COMMAND" "$SERVICE_NAME" fi } break_end() { echo -e "${gl_lv}操作完成${gl_bai}" echo "按任意键继续..." read -n 1 -s -r -p "" echo "" clear } ip_address() { get_public_ip() { curl -s https://ipinfo.io/ip && echo } get_local_ip() { ip route get 8.8.8.8 2>/dev/null | grep -oP 'src \K[^ ]+' || \ hostname -I 2>/dev/null | awk '{print $1}' || \ ifconfig 2>/dev/null | grep -E 'inet [0-9]' | grep -v '127.0.0.1' | awk '{print $2}' | head -n1 } public_ip=$(get_public_ip) isp_info=$(curl -s --max-time 3 http://ipinfo.io/org) if echo "$isp_info" | grep -Eiq 'CHINANET|mobile|unicom|telecom'; then ipv4_address=$(get_local_ip) else ipv4_address="$public_ip" fi # ipv4_address=$(curl -s https://ipinfo.io/ip && echo) ipv6_address=$(curl -s --max-time 1 https://v6.ipinfo.io/ip && echo) } output_status() { output=$(awk 'BEGIN { rx_total = 0; tx_total = 0 } $1 ~ /^(eth|ens|enp|eno)[0-9]+/ { rx_total += $2 tx_total += $10 } END { rx_units = "Bytes"; tx_units = "Bytes"; if (rx_total > 1024) { rx_total /= 1024; rx_units = "K"; } if (rx_total > 1024) { rx_total /= 1024; rx_units = "M"; } if (rx_total > 1024) { rx_total /= 1024; rx_units = "G"; } if (tx_total > 1024) { tx_total /= 1024; tx_units = "K"; } if (tx_total > 1024) { tx_total /= 1024; tx_units = "M"; } if (tx_total > 1024) { tx_total /= 1024; tx_units = "G"; } printf("%.2f%s %.2f%s\n", rx_total, rx_units, tx_total, tx_units); }' /proc/net/dev) rx=$(echo "$output" | awk '{print $1}') tx=$(echo "$output" | awk '{print $2}') } current_timezone() { if grep -q 'Alpine' /etc/issue; then date +"%Z %z" else timedatectl | grep "Time zone" | awk '{print $3}' fi } # 修复dpkg中断问题 fix_dpkg() { pkill -9 -f 'apt|dpkg' rm -f /var/lib/dpkg/lock-frontend /var/lib/dpkg/lock DEBIAN_FRONTEND=noninteractive dpkg --configure -a } check_crontab_installed() { if ! command -v crontab >/dev/null 2>&1; then install_crontab fi } install_crontab() { local package_manager if [ -f /etc/os-release ]; then . /etc/os-release case "$ID" in ubuntu|debian|kali) apt update apt install -y cron systemctl enable cron systemctl start cron ;; centos|rhel|almalinux|rocky|fedora) if command -v dnf >/dev/null 2>&1; then package_manager=dnf elif command -v yum >/dev/null 2>&1; then package_manager=yum else echo "错误: 未找到 DNF/YUM，无法安装 cronie" return 1 fi "$package_manager" install -y cronie || return 1 /bin/systemctl enable --now crond.service || return 1 command -v crontab >/dev/null 2>&1 || return 1 /bin/systemctl is-active --quiet crond.service || return 1 ;; alpine) apk add --no-cache cronie rc-update add crond rc-service crond start ;; arch|manjaro) pacman -S --noconfirm cronie systemctl enable cronie systemctl start cronie ;; opensuse|suse|opensuse-tumbleweed) zypper install -y cron systemctl enable cron systemctl start cron ;; iStoreOS|openwrt|ImmortalWrt|lede) opkg update opkg install cron /etc/init.d/cron enable /etc/init.d/cron start ;; FreeBSD) pkg install -y cronie sysrc cron_enable="YES" service cron start ;; *) echo "不支持的发行版: $ID" return ;; esac else echo "无法确定操作系统。" return fi command -v crontab >/dev/null 2>&1 || return 1 echo -e "${gl_lv}crontab 已安装且 cron 服务正在运行。${gl_bai}" } CheckFirstRun_false() { if grep -q '^permission_granted="false"' /usr/local/bin/k > /dev/null 2>&1; then UserLicenseAgreement fi } # 提示用户同意条款 UserLicenseAgreement() { clear echo -e "${gl_kjlan}欢迎使用生物信息学脚本工具箱${gl_bai}" echo "首次使用脚本，请先阅读并同意用户许可协议。" echo "用户许可协议: ${dist_base}/AGREEMENT.txt" echo -e "----------------------" read -e -p "是否同意以上条款？(y/n): " user_input if [ "$user_input" = "y" ] || [ "$user_input" = "Y" ]; then sed -i 's/^permission_granted="false"/permission_granted="true"/' ~/kejilion.sh sed -i 's/^permission_granted="false"/permission_granted="true"/' /usr/local/bin/k else clear exit fi } # ---------------------------- # 1. 系统信息查询 # ---------------------------- linux_info() { clear echo -e "${gl_kjlan}正在查询系统信息……${gl_bai}" ip_address local cpu_info=$(lscpu | awk -F': +' '/Model name:/ {print $2; exit}') local cpu_usage_percent=$(awk '{u=$2+$4; t=$2+$4+$5; if (NR==1){u1=u; t1=t;} else printf "%.0f\n", (($2+$4-u1) * 100 / (t-t1))}' \ <(grep 'cpu ' /proc/stat) <(sleep 1; grep 'cpu ' /proc/stat)) local cpu_cores=$(nproc) local cpu_freq=$(cat /proc/cpuinfo | grep "MHz" | head -n 1 | awk '{printf "%.1f GHz\n", $4/1000}') local mem_info=$(free -b | awk 'NR==2{printf "%.2f/%.2fM (%.2f%%)", $3/1024/1024, $2/1024/1024, $3*100/$2}') local disk_info=$(df -h | awk '$NF=="/"{printf "%s/%s (%s)", $3, $2, $5}') local ipinfo=$(curl -s ipinfo.io) local country=$(echo "$ipinfo" | grep 'country' | awk -F': ' '{print $2}' | tr -d '",') local city=$(echo "$ipinfo" | grep 'city' | awk -F': ' '{print $2}' | tr -d '",') local isp_info=$(echo "$ipinfo" | grep 'org' | awk -F': ' '{print $2}' | tr -d '",') local load=$(uptime | awk '{print $(NF-2), $(NF-1), $NF}') local dns_addresses=$(awk '/^nameserver/{printf "%s ", $2} END {print ""}' /etc/resolv.conf) local cpu_arch=$(uname -m) local hostname=$(uname -n) local kernel_version=$(uname -r) local congestion_algorithm=$(sysctl -n net.ipv4.tcp_congestion_control) local queue_algorithm=$(sysctl -n net.core.default_qdisc) local os_info=$(grep PRETTY_NAME /etc/os-release | cut -d '=' -f2 | tr -d '"') output_status local current_time=$(date "+%Y-%m-%d %I:%M %p") local swap_info=$(free -m | awk 'NR==3{used=$3; total=$2; if (total == 0) {percentage=0} else {percentage=used*100/total}; printf "%dM/%dM (%d%%)", used, total, percentage}') local runtime=$(cat /proc/uptime | awk -F. '{run_days=int($1 / 86400);run_hours=int(($1 % 86400) / 3600);run_minutes=int(($1 % 3600) / 60); if (run_days > 0) printf("%d天 ", run_days); if (run_hours > 0) printf("%d时 ", run_hours); printf("%d分\n", run_minutes)}') local timezone=$(current_timezone) local tcp_count=$(ss -t | wc -l) local udp_count=$(ss -u | wc -l) clear echo -e "系统信息查询" echo -e "${gl_kjlan}-------------" echo -e "${gl_kjlan}主机名: ${gl_bai}$hostname" echo -e "${gl_kjlan}系统版本: ${gl_bai}$os_info" echo -e "${gl_kjlan}Linux版本: ${gl_bai}$kernel_version" echo -e "${gl_kjlan}-------------" echo -e "${gl_kjlan}CPU架构: ${gl_bai}$cpu_arch" echo -e "${gl_kjlan}CPU型号: ${gl_bai}$cpu_info" echo -e "${gl_kjlan}CPU核心数: ${gl_bai}$cpu_cores" echo -e "${gl_kjlan}CPU频率: ${gl_bai}$cpu_freq" echo -e "${gl_kjlan}-------------" echo -e "${gl_kjlan}CPU占用: ${gl_bai}$cpu_usage_percent%" echo -e "${gl_kjlan}系统负载: ${gl_bai}$load" echo -e "${gl_kjlan}TCP|UDP连接数: ${gl_bai}$tcp_count|$udp_count" echo -e "${gl_kjlan}物理内存: ${gl_bai}$mem_info" echo -e "${gl_kjlan}虚拟内存: ${gl_bai}$swap_info" echo -e "${gl_kjlan}硬盘占用: ${gl_bai}$disk_info" echo -e "${gl_kjlan}-------------" echo -e "${gl_kjlan}总接收: ${gl_bai}$rx" echo -e "${gl_kjlan}总发送: ${gl_bai}$tx" echo -e "${gl_kjlan}-------------" echo -e "${gl_kjlan}网络算法: ${gl_bai}$congestion_algorithm $queue_algorithm" echo -e "${gl_kjlan}-------------" echo -e "${gl_kjlan}运营商: ${gl_bai}$isp_info" if [ -n "$ipv4_address" ]; then echo -e "${gl_kjlan}IPv4地址: ${gl_bai}$ipv4_address" fi if [ -n "$ipv6_address" ]; then echo -e "${gl_kjlan}IPv6地址: ${gl_bai}$ipv6_address" fi echo -e "${gl_kjlan}DNS地址: ${gl_bai}$dns_addresses" echo -e "${gl_kjlan}地理位置: ${gl_bai}$country $city" echo -e "${gl_kjlan}系统时间: ${gl_bai}$timezone $current_time" echo -e "${gl_kjlan}-------------" echo -e "${gl_kjlan}运行时长: ${gl_bai}$runtime" echo } # ---------------------------- # 2. 系统更新 # ---------------------------- linux_update() { echo -e "${gl_kjlan}正在系统更新...${gl_bai}" if command -v dnf &>/dev/null; then dnf -y update elif command -v yum &>/dev/null; then yum -y update elif command -v apt &>/dev/null; then fix_dpkg DEBIAN_FRONTEND=noninteractive apt update -y DEBIAN_FRONTEND=noninteractive apt full-upgrade -y elif command -v apk &>/dev/null; then apk update && apk upgrade elif command -v pacman &>/dev/null; then pacman -Syu --noconfirm elif command -v zypper &>/dev/null; then zypper refresh zypper update elif command -v opkg &>/dev/null; then opkg update else echo "未知的包管理器!" return fi } # ---------------------------- # 3. 系统清理 # ---------------------------- linux_clean() { echo -e "${gl_kjlan}正在系统清理...${gl_bai}" if command -v dnf &>/dev/null; then rpm --rebuilddb dnf autoremove -y dnf clean all dnf makecache journalctl --rotate journalctl --vacuum-time=1s journalctl --vacuum-size=500M elif command -v yum &>/dev/null; then rpm --rebuilddb yum autoremove -y yum clean all yum makecache journalctl --rotate journalctl --vacuum-time=1s journalctl --vacuum-size=500M elif command -v apt &>/dev/null; then fix_dpkg apt autoremove --purge -y apt clean -y apt autoclean -y journalctl --rotate journalctl --vacuum-time=1s journalctl --vacuum-size=500M elif command -v apk &>/dev/null; then echo "清理包管理器缓存..." apk cache clean echo "删除系统日志..." rm -rf /var/log/* echo "删除APK缓存..." rm -rf /var/cache/apk/* echo "删除临时文件..." rm -rf /tmp/* elif command -v pacman &>/dev/null; then pacman -Rns $(pacman -Qdtq) --noconfirm pacman -Scc --noconfirm journalctl --rotate journalctl --vacuum-time=1s journalctl --vacuum-size=500M elif command -v zypper &>/dev/null; then zypper clean --all zypper refresh journalctl --rotate journalctl --vacuum-time=1s journalctl --vacuum-size=500M elif command -v opkg &>/dev/null; then echo "删除系统日志..." rm -rf /var/log/* echo "删除临时文件..." rm -rf /tmp/* elif command -v pkg &>/dev/null; then echo "清理未使用的依赖..." pkg autoremove -y echo "清理包管理器缓存..." pkg clean -y echo "删除系统日志..." rm -rf /var/log/* echo "删除临时文件..." rm -rf /tmp/* else echo "未知的包管理器!" return fi return } # ---------------------------- # 4. 生物信息环境搭建（PspC 推荐安装清单） # 目标系统 Ubuntu 24.04 LTS，清单：Python 3.10(Conda)、Biopython、SignalP 6.0h、 # CD-HIT 4.8.1、MAFFT 7.526、IQ-TREE 3.1.3、R 4.4+、基础编译环境。 # ConSurf 使用 Web Server，无需本地安装。 # ---------------------------- bio_env_name="bioinfo" bio_python_ver="3.10" bio_cdhit_ver="4.8.1" bio_mafft_ver="7.526" bio_iqtree_ver="3.1.3" bio_r_minver="4.4" bio_sigp_ver="6.0h" bio_dist_bio="${dist_base}/bio" bio_apt_updated="0" bio_init_paths() { if [ "$(id -u)" -eq 0 ]; then bio_conda_dir="/opt/miniconda3" bio_work_dir="/opt/bioinfo-setup" elif [ -d "$HOME/miniconda3" ] || [ ! -d "/opt/miniconda3" ]; then bio_conda_dir="$HOME/miniconda3" bio_work_dir="$HOME/.bioinfo-setup" else # 管理员已把 Miniconda 装在 /opt，普通用户直接复用 bio_conda_dir="/opt/miniconda3" bio_work_dir="$HOME/.bioinfo-setup" fi bio_env_bin="$bio_conda_dir/envs/$bio_env_name/bin" bio_log_file="$bio_work_dir/install.log" mkdir -p "$bio_work_dir" } bio_sudo() { if [ "$(id -u)" -eq 0 ]; then "$@" elif command -v sudo >/dev/null 2>&1; then sudo "$@" else "$@" fi } bio_apt_ready() { [ "$bio_apt_updated" = "1" ] && return 0 if command -v apt >/dev/null 2>&1; then if [ "$(id -u)" -eq 0 ]; then fix_dpkg >/dev/null 2>&1 env DEBIAN_FRONTEND=noninteractive apt update -y elif command -v sudo >/dev/null 2>&1; then sudo env DEBIAN_FRONTEND=noninteractive apt update -y else env DEBIAN_FRONTEND=noninteractive apt update -y fi bio_apt_updated="1" fi } bio_apt_install() { bio_apt_ready bio_sudo env DEBIAN_FRONTEND=noninteractive apt install -y "$@" } bio_fetch() { # bio_fetch <保存路径> [备用URL]：断点续传 + 多次重试，应对下载中途断流 local out="$1" url="$2" mirror="$3" attempt mkdir -p "$(dirname "$out")" for attempt in 1 2 3; do if [ "$attempt" -gt 1 ] && [ -s "$out" ]; then curl -sSfL -C - --retry 2 --retry-delay 2 --connect-timeout 15 --max-time 1800 -o "$out" "$url" && return 0 else curl -sSfL --retry 2 --retry-delay 2 --connect-timeout 15 --max-time 1800 -o "$out" "$url" && return 0 fi [ "$attempt" -lt 3 ] && sleep 2 done if [ -n "$mirror" ]; then echo -e "${gl_huang}官方源下载失败，尝试备用源……${gl_bai}" for attempt in 1 2 3; do if [ "$attempt" -gt 1 ] && [ -s "$out" ]; then curl -sSfL -C - --retry 2 --retry-delay 2 --connect-timeout 15 --max-time 1800 -o "$out" "$mirror" && return 0 else curl -sSfL --retry 2 --retry-delay 2 --connect-timeout 15 --max-time 1800 -o "$out" "$mirror" && return 0 fi [ "$attempt" -lt 3 ] && sleep 2 done fi return 1 } bio_logged() { # bio_logged <描述> <函数> [参数...]：屏幕同步显示的同时，把完整输出落盘到安装日志 local label="$1" rc=0 fifo tee_pid shift mkdir -p "$bio_work_dir" 2>/dev/null # 日志超过 5MB 时只保留末尾 2000 行，防止无限膨胀 if [ -f "$bio_log_file" ] && [ "$(wc -c < "$bio_log_file" 2>/dev/null || echo 0)" -gt 5242880 ]; then tail -n 2000 "$bio_log_file" > "$bio_log_file.tmp" 2>/dev/null && mv -f "$bio_log_file.tmp" "$bio_log_file" fi { echo "" echo "===== $(date '+%Y-%m-%d %H:%M:%S') 开始: $label =====" } >> "$bio_log_file" 2>/dev/null # FIFO + tee：输出实时上屏，wait 保证函数返回前日志已完整落盘 fifo="$bio_work_dir/.logfifo.$$" mkfifo "$fifo" 2>/dev/null || fifo="" if [ -n "$fifo" ]; then tee -a "$bio_log_file" < "$fifo" & tee_pid=$! "$@" > "$fifo" 2>&1 || rc=$? wait "$tee_pid" rm -f "$fifo" else # mkfifo 不可用时退化为仅落盘（无实时上屏） "$@" >> "$bio_log_file" 2>&1 || rc=$? fi echo "===== $(date '+%Y-%m-%d %H:%M:%S') 结束: $label (退出码 $rc) =====" >> "$bio_log_file" 2>/dev/null return $rc } bio_ver_ge() { # bio_ver_ge <当前版本> <最低版本>，基于 sort -V 比较 [ "$(printf '%s\n%s\n' "${1:-0}" "$2" | sort -V | head -n 1)" = "$2" ] } bio_register_path() { # 把指定 bin 目录写入登录配置，保证可执行程序加入 PATH local bin_dir="$1" local line="export PATH=\"$bin_dir:\$PATH\"" if [ "$(id -u)" -eq 0 ] && [ -d /etc/profile.d ]; then echo "$line" > /etc/profile.d/bioinfo.sh fi if ! grep -qF '# bioinfo-env' ~/.bashrc 2>/dev/null; then { echo ""; echo "$line # bioinfo-env"; } >> ~/.bashrc fi } bio_require_env() { if [ ! -x "$bio_env_bin/python" ]; then echo -e "${gl_huang}未检测到 $bio_env_name Python 环境，先自动安装 Miniconda + Python $bio_python_ver ……${gl_bai}" bio_install_conda || return 1 fi bio_register_path "$bio_env_bin" export PATH="$bio_env_bin:$PATH" } bio_pip_install() { # 优先官方 PyPI，失败自动切换清华 TUNA 镜像 if "$bio_env_bin/pip" install "$@"; then return 0 fi echo -e "${gl_huang}PyPI 官方源安装失败，切换清华 TUNA 镜像重试……${gl_bai}" "$bio_env_bin/pip" install -i https://pypi.tuna.tsinghua.edu.cn/simple "$@" } bio_install_conda() { local arch installer_url mirror_url tmp_sh case "$(uname -m)" in x86_64) arch="x86_64" ;; aarch64|arm64) arch="aarch64" ;; *) echo -e "${gl_hong}不支持的 CPU 架构: $(uname -m)${gl_bai}" return 1 ;; esac if [ ! -x "$bio_conda_dir/bin/conda" ]; then echo -e "${gl_kjlan}安装 Miniconda 到 $bio_conda_dir ……${gl_bai}" installer_url="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-$arch.sh" mirror_url="https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-$arch.sh" tmp_sh="$bio_work_dir/miniconda.sh" if ! bio_fetch "$tmp_sh" "$installer_url" "$mirror_url"; then echo -e "${gl_hong}Miniconda 下载失败，请检查网络后重试${gl_bai}" return 1 fi if ! bash "$tmp_sh" -b -p "$bio_conda_dir"; then echo -e "${gl_hong}Miniconda 安装失败（目录不可写？）${gl_bai}" return 1 fi rm -f "$tmp_sh" else echo -e "${gl_lv}Miniconda 已存在：$bio_conda_dir${gl_bai}" fi if [ -x "$bio_env_bin/python" ] && "$bio_env_bin/python" -c 'import sys; sys.exit(0 if sys.version_info[:2] == (3, 10) else 1)' 2>/dev/null; then echo -e "${gl_lv}Python $bio_python_ver 环境已就绪：$bio_env_bin${gl_bai}" else if [ -d "$bio_conda_dir/envs/$bio_env_name" ]; then echo -e "${gl_huang}检测到旧的 $bio_env_name 环境（不完整或 Python 版本不符），正在重建……${gl_bai}" "$bio_conda_dir/bin/conda" env remove -y -n "$bio_env_name" >/dev/null 2>&1 rm -rf "$bio_conda_dir/envs/$bio_env_name" fi echo -e "${gl_kjlan}创建 conda 虚拟环境 $bio_env_name（Python $bio_python_ver）……${gl_bai}" if ! "$bio_conda_dir/bin/conda" create -y -n "$bio_env_name" "python=$bio_python_ver"; then echo -e "${gl_huang}conda 官方源创建失败，写入清华 TUNA 镜像后重试……${gl_bai}" cat > "$bio_conda_dir/.condarc" 2>/dev/null <&1)（$bio_env_bin）${gl_bai}" echo -e "重新登录后 PATH 自动生效，当前会话已可直接使用。" } bio_install_biopython() { bio_require_env || return 1 if "$bio_env_bin/python" -c 'import Bio' >/dev/null 2>&1; then echo -e "${gl_lv}Biopython 已安装：v$("$bio_env_bin/python" -c 'import Bio; print(Bio.__version__)' 2>/dev/null)${gl_bai}" return 0 fi echo -e "${gl_kjlan}安装 Biopython ……${gl_bai}" if ! bio_pip_install biopython; then echo -e "${gl_hong}Biopython 安装失败${gl_bai}" return 1 fi echo -e "${gl_lv}Biopython 安装完成：v$("$bio_env_bin/python" -c 'import Bio; print(Bio.__version__)' 2>/dev/null)${gl_bai}" } bio_install_signalp() { bio_require_env || return 1 # 已安装且模型权重齐全则跳过 local sigp_dir sigp_dir=$("$bio_env_bin/python" -c 'import signalp, os; print(os.path.dirname(signalp.__file__))' 2>/dev/null) if [ -x "$bio_env_bin/signalp" ] && [ -n "$sigp_dir" ] && [ -n "$(ls -A "$sigp_dir/model_weights" 2>/dev/null)" ]; then echo -e "${gl_lv}SignalP 已安装：$("$bio_env_bin/signalp" --version 2>&1 | head -n 1)${gl_bai}" return 0 fi echo -e "${gl_huang}SignalP $bio_sigp_ver 由丹麦技术大学（DTU）发布，仅限学术研究使用。${gl_bai}" echo -e "继续安装即表示你已确认符合 DTU 学术使用许可。" read -e -p "是否继续？(y/n): " bio_yn case "$bio_yn" in y|Y) ;; *) echo "已取消，可稍后在菜单中单独重试。" return 1 ;; esac local tarball="$bio_work_dir/signalp-$bio_sigp_ver.tar.gz" local models_tar="$bio_work_dir/signalp-$bio_sigp_ver.models.tar.gz" # DTU 官网需人工申请下载，包体由校内分发服务器或用户手动放置提供 if [ ! -s "$tarball" ]; then echo -e "${gl_kjlan}下载 SignalP $bio_sigp_ver 安装包（校内源）……${gl_bai}" if ! bio_fetch "$tarball" "$bio_dist_bio/signalp-$bio_sigp_ver.tar.gz"; then echo -e "${gl_hong}无法自动获取 SignalP 安装包。${gl_bai}" echo -e "请访问 ${gl_huang}https://services.healthtech.dtu.dk/services/SignalP-6.0/${gl_bai} Downloads 页签，" echo -e "填写姓名/邮箱并同意学术许可后，下载以下两个文件并放到 ${gl_huang}$bio_work_dir/${gl_bai}（保持文件名不变）：" echo -e " 1. signalp-$bio_sigp_ver.tar.gz" echo -e " 2. signalp-$bio_sigp_ver.models.tar.gz" echo -e "放置后重新运行本项，脚本会自动完成剩余步骤。" echo -e "管理员也可把两个包上传到 ${gl_huang}$bio_dist_bio/${gl_bai}，全校即可一键自动安装。" return 1 fi fi if [ ! -s "$models_tar" ]; then echo -e "${gl_kjlan}下载 SignalP 模型权重包（校内源）……${gl_bai}" bio_fetch "$models_tar" "$bio_dist_bio/signalp-$bio_sigp_ver.models.tar.gz" || rm -f "$models_tar" if [ ! -s "$models_tar" ]; then echo -e "${gl_hong}模型权重包获取失败，请手动下载 signalp-$bio_sigp_ver.models.tar.gz 放到 ${gl_huang}$bio_work_dir/${gl_bai}" return 1 fi fi echo -e "${gl_kjlan}安装依赖（numpy <2 + CPU 版 PyTorch，体积较大，请耐心等待）……${gl_bai}" bio_pip_install "numpy<2" || return 1 if ! "$bio_env_bin/pip" install torch --index-url https://download.pytorch.org/whl/cpu 2>/dev/null; then echo -e "${gl_huang}PyTorch CPU 专用源失败，改用 PyPI……${gl_bai}" bio_pip_install torch || return 1 fi echo -e "${gl_kjlan}安装 SignalP Python 包 ……${gl_bai}" local pkg_dir="$bio_work_dir/signalp-6-package" rm -rf "$pkg_dir" tar -zxf "$tarball" -C "$bio_work_dir" || { echo -e "${gl_hong}SignalP 安装包解压失败${gl_bai}"; return 1; } [ -d "$pkg_dir" ] || pkg_dir=$(find "$bio_work_dir" -maxdepth 1 -type d -name 'signalp*6*' ! -name '*models*' 2>/dev/null | head -n 1) if [ -z "$pkg_dir" ] || [ ! -d "$pkg_dir" ]; then echo -e "${gl_hong}未找到 SignalP 包目录，解压结果异常${gl_bai}" return 1 fi bio_pip_install "$pkg_dir/" || { echo -e "${gl_hong}SignalP pip 安装失败${gl_bai}"; return 1; } echo -e "${gl_kjlan}放置模型权重文件……${gl_bai}" sigp_dir=$("$bio_env_bin/python" -c 'import signalp, os; print(os.path.dirname(signalp.__file__))' 2>/dev/null) if [ -z "$sigp_dir" ]; then echo -e "${gl_hong}无法定位 signalp 包目录，请手动放置模型权重${gl_bai}" return 1 fi tar -zxf "$models_tar" -C "$bio_work_dir" || { echo -e "${gl_hong}模型权重解压失败${gl_bai}"; return 1; } local models_src="" [ -d "$pkg_dir/models" ] && models_src="$pkg_dir/models" [ -z "$models_src" ] && [ -d "$bio_work_dir/models" ] && models_src="$bio_work_dir/models" if [ -z "$models_src" ] || [ -z "$(ls -A "$models_src" 2>/dev/null)" ]; then echo -e "${gl_hong}未在压缩包中找到模型权重目录${gl_bai}" return 1 fi mkdir -p "$sigp_dir/model_weights" mv -f "$models_src"/* "$sigp_dir/model_weights/" || { echo -e "${gl_hong}模型权重移动失败${gl_bai}"; return 1; } if "$bio_env_bin/signalp" --version >/dev/null 2>&1; then echo -e "${gl_lv}SignalP 安装完成：$("$bio_env_bin/signalp" --version 2>&1 | head -n 1)${gl_bai}" else echo -e "${gl_hong}SignalP 安装后验证失败，请检查上方日志${gl_bai}" return 1 fi } bio_install_cdhit() { if command -v cd-hit >/dev/null 2>&1; then local cur cur=$(cd-hit -h 2>&1 | grep -oiE 'version [0-9.]+' | head -n 1 | grep -oE '[0-9]+\.[0-9.]+') if bio_ver_ge "$cur" "$bio_cdhit_ver"; then echo -e "${gl_lv}CD-HIT 已安装：v$cur${gl_bai}" return 0 fi echo -e "${gl_huang}CD-HIT 版本低于 $bio_cdhit_ver（当前 ${cur:-未知}），尝试升级……${gl_bai}" fi echo -e "${gl_kjlan}通过 apt 安装 CD-HIT $bio_cdhit_ver ……${gl_bai}" bio_apt_install cd-hit || { echo -e "${gl_hong}CD-HIT 安装失败${gl_bai}"; return 1; } local new_ver new_ver=$(cd-hit -h 2>&1 | grep -oiE 'version [0-9.]+' | head -n 1 | grep -oE '[0-9]+\.[0-9.]+') echo -e "${gl_lv}CD-HIT 安装完成：v${new_ver:-未知}${gl_bai}" } bio_install_mafft() { if command -v mafft >/dev/null 2>&1; then local cur cur=$(mafft --version 2>&1 | grep -oE '[0-9]+\.[0-9]+' | head -n 1) if bio_ver_ge "$cur" "$bio_mafft_ver"; then echo -e "${gl_lv}MAFFT 已安装：v$cur${gl_bai}" return 0 fi echo -e "${gl_huang}MAFFT 版本低于 $bio_mafft_ver（当前 ${cur:-未知}），尝试升级……${gl_bai}" fi echo -e "${gl_kjlan}通过 apt 安装 MAFFT ……${gl_bai}" bio_apt_install mafft || { echo -e "${gl_hong}MAFFT 安装失败${gl_bai}"; return 1; } local new_ver new_ver=$(mafft --version 2>&1 | grep -oE '[0-9]+\.[0-9]+' | head -n 1) if bio_ver_ge "$new_ver" "$bio_mafft_ver"; then echo -e "${gl_lv}MAFFT 安装完成：v$new_ver${gl_bai}" return 0 fi # apt 源版本不足时回退 MAFFT 官方 deb（仅提供 x86_64） if [ "$(uname -m)" != "x86_64" ]; then echo -e "${gl_huang}系统源 MAFFT 版本为 ${new_ver:-未知}，官方 deb 仅支持 x86_64，请手动确认${gl_bai}" return 1 fi echo -e "${gl_kjlan}改用 MAFFT 官方 $bio_mafft_ver deb 包安装（系统源版本：${new_ver:-未知}）……${gl_bai}" local deb="$bio_work_dir/mafft_${bio_mafft_ver}-1_amd64.deb" if ! bio_fetch "$deb" "https://mafft.cbrc.jp/alignment/software/mafft_${bio_mafft_ver}-1_amd64.deb"; then echo -e "${gl_hong}MAFFT 官方包下载失败${gl_bai}" return 1 fi bio_apt_install "$deb" || { echo -e "${gl_hong}MAFFT deb 安装失败${gl_bai}"; return 1; } echo -e "${gl_lv}MAFFT 安装完成：$(mafft --version 2>&1 | head -n 1)${gl_bai}" } bio_install_iqtree() { if command -v iqtree3 >/dev/null 2>&1; then local cur cur=$(iqtree3 --version 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n 1) if [ "$cur" = "$bio_iqtree_ver" ]; then echo -e "${gl_lv}IQ-TREE 已安装：v$cur${gl_bai}" return 0 fi fi local arch candidates c tarball url case "$(uname -m)" in x86_64) arch="intel" ;; aarch64|arm64) arch="arm" ;; *) echo -e "${gl_hong}不支持的 CPU 架构: $(uname -m)${gl_bai}" return 1 ;; esac # 官方仓库为 iqtree/iqtree3，资产名随版本变化，依次尝试候选包 if [ "$arch" = "intel" ]; then candidates="iqtree-$bio_iqtree_ver-Linux-intel.tar.gz iqtree-$bio_iqtree_ver-Linux.tar.gz" else candidates="iqtree-$bio_iqtree_ver-Linux-arm.tar.gz iqtree-$bio_iqtree_ver-Linux.tar.gz" fi tarball="" for c in $candidates; do url="https://github.com/iqtree/iqtree3/releases/download/v$bio_iqtree_ver/$c" echo -e "${gl_kjlan}下载 IQ-TREE $bio_iqtree_ver 官方二进制：$c ……${gl_bai}" if bio_fetch "$bio_work_dir/$c" "$url"; then tarball="$bio_work_dir/$c" break fi rm -f "$bio_work_dir/$c" done if [ -z "$tarball" ]; then echo -e "${gl_hong}IQ-TREE 下载失败，请检查网络或手动下载后安装：${gl_bai}" echo -e " https://github.com/iqtree/iqtree3/releases/tag/v$bio_iqtree_ver" return 1 fi local ext_dir="$bio_work_dir/iqtree-extract" rm -rf "$ext_dir" mkdir -p "$ext_dir" tar -zxf "$tarball" -C "$ext_dir" || { echo -e "${gl_hong}IQ-TREE 解压失败${gl_bai}"; return 1; } local src_bin src_bin=$(find "$ext_dir" -type f -name 'iqtree3*' ! -name '*static*' 2>/dev/null | head -n 1) if [ -z "$src_bin" ]; then echo -e "${gl_hong}未在压缩包中找到 IQ-TREE 可执行文件${gl_bai}" return 1 fi local dest_dir if [ "$(id -u)" -eq 0 ] || [ -w /usr/local/bin ]; then dest_dir="/usr/local/bin" else dest_dir="$HOME/.local/bin" mkdir -p "$dest_dir" case ":$PATH:" in *":$dest_dir:"*) ;; *) bio_register_path "$dest_dir" export PATH="$dest_dir:$PATH" ;; esac fi bio_sudo cp -f "$src_bin" "$dest_dir/iqtree3" || { echo -e "${gl_hong}IQ-TREE 部署失败${gl_bai}"; return 1; } bio_sudo chmod 755 "$dest_dir/iqtree3" bio_sudo ln -sf "$dest_dir/iqtree3" "$dest_dir/iqtree" 2>/dev/null hash -r echo -e "${gl_lv}IQ-TREE 安装完成：$(iqtree3 --version 2>&1 | head -n 1)${gl_bai}" } bio_install_r() { if command -v R >/dev/null 2>&1; then local cur cur=$(R --version 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n 1) if bio_ver_ge "$cur" "$bio_r_minver"; then echo -e "${gl_lv}R 已安装：v$cur${gl_bai}" return 0 fi echo -e "${gl_huang}R 版本低于 $bio_r_minver（当前 ${cur:-未知}），尝试升级……${gl_bai}" fi if ! command -v apt >/dev/null 2>&1; then # 非 apt 发行版走通用安装 if command -v dnf >/dev/null 2>&1; then bio_sudo dnf install -y R && echo -e "${gl_lv}R 安装完成：$(R --version 2>&1 | head -n 1)${gl_bai}" && return 0 elif command -v yum >/dev/null 2>&1; then bio_sudo yum install -y R && echo -e "${gl_lv}R 安装完成：$(R --version 2>&1 | head -n 1)${gl_bai}" && return 0 fi echo -e "${gl_hong}无法识别包管理器，请手动安装 R${gl_bai}" return 1 fi # Ubuntu/Debian：系统源自带版本偏旧，先走 CRAN 官方源拿 4.4+ local codename codename=$(grep -E '^VERSION_CODENAME=' /etc/os-release 2>/dev/null | cut -d= -f2) if [ -n "$codename" ]; then echo -e "${gl_kjlan}添加 CRAN 官方 apt 源（$codename-cran40）安装 R $bio_r_minver+ ……${gl_bai}" bio_apt_install curl ca-certificates gpg >/dev/null 2>&1 bio_sudo mkdir -p /etc/apt/keyrings if curl -fsSL --connect-timeout 15 --max-time 60 "https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc" | bio_sudo tee /etc/apt/keyrings/cran40.asc >/dev/null && echo "deb [signed-by=/etc/apt/keyrings/cran40.asc] https://cloud.r-project.org/bin/linux/ubuntu ${codename}-cran40/" | bio_sudo tee /etc/apt/sources.list.d/cran40.list >/dev/null; then bio_apt_updated="0" bio_apt_ready if bio_apt_install r-base; then local rv rv=$(R --version 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n 1) echo -e "${gl_lv}R 安装完成：v${rv:-未知}${gl_bai}" return 0 fi fi echo -e "${gl_huang}CRAN 源配置失败，回退系统 apt 源安装……${gl_bai}" fi if bio_apt_install r-base; then local rv2 rv2=$(R --version 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n 1) if bio_ver_ge "$rv2" "$bio_r_minver"; then echo -e "${gl_lv}R 安装完成：v$rv2${gl_bai}" else echo -e "${gl_huang}R 已安装但版本 v${rv2:-未知} 低于建议的 $bio_r_minver.x，请按需手动升级${gl_bai}" fi return 0 fi echo -e "${gl_hong}R 安装失败${gl_bai}" return 1 } bio_install_buildtools() { echo -e "${gl_kjlan}安装基础编译环境及常用依赖……${gl_bai}" if command -v apt >/dev/null 2>&1; then bio_apt_install build-essential gcc g++ make wget curl git unzip bzip2 xz-utils ca-certificates file pkg-config perl || { echo -e "${gl_hong}基础编译环境安装失败${gl_bai}" return 1 } elif command -v dnf >/dev/null 2>&1; then bio_sudo dnf install -y gcc gcc-c++ make wget curl git unzip bzip2 xz-utils file perl elif command -v yum >/dev/null 2>&1; then bio_sudo yum install -y gcc gcc-c++ make wget curl git unzip bzip2 xz-utils file perl else echo -e "${gl_hong}暂不支持该发行版，请手动安装 gcc/make/wget/curl/git${gl_bai}" return 1 fi echo -e "${gl_lv}基础编译环境就绪：gcc $(gcc -dumpversion 2>/dev/null)、$(git --version 2>/dev/null)${gl_bai}" } bio_row() { # bio_row <组件名> <0=已装/1=未装> <版本信息> if [ "$2" = "0" ]; then echo -e " ${gl_lv}[已安装]${gl_bai} $1 ${gl_huang}$3${gl_bai}" else echo -e " ${gl_hong}[未安装]${gl_bai} $1" fi } bio_check_status() { bio_init_paths local cur echo -e "${gl_kjlan}生物信息学分析环境体检（PspC 清单）${gl_bai}" echo "----------------------------------------" if [ -x "$bio_env_bin/python" ]; then local path_state case ":$PATH:" in *":$bio_env_bin:"*) path_state="PATH 已生效" ;; *) path_state="PATH 重新登录后生效" ;; esac bio_row "Miniconda + Python $bio_python_ver（$bio_env_name 环境）" 0 "$("$bio_env_bin/python" --version 2>&1)，$path_state" else bio_row "Miniconda + Python $bio_python_ver（$bio_env_name 环境）" 1 fi if "$bio_env_bin/python" -c 'import Bio' >/dev/null 2>&1; then bio_row "Biopython（FASTA 读取/序列处理）" 0 "v$("$bio_env_bin/python" -c 'import Bio; print(Bio.__version__)' 2>/dev/null)" else bio_row "Biopython（FASTA 读取/序列处理）" 1 fi if [ -x "$bio_env_bin/signalp" ]; then bio_row "SignalP $bio_sigp_ver（信号肽预测）" 0 "$("$bio_env_bin/signalp" --version 2>&1 | head -n 1)" else bio_row "SignalP $bio_sigp_ver（信号肽预测）" 1 fi if command -v cd-hit >/dev/null 2>&1; then cur=$(cd-hit -h 2>&1 | grep -oiE 'version [0-9.]+' | head -n 1 | grep -oE '[0-9]+\.[0-9.]+') bio_row "CD-HIT（序列去冗余）" 0 "v${cur:-未知}" else bio_row "CD-HIT（序列去冗余）" 1 fi if command -v mafft >/dev/null 2>&1; then cur=$(mafft --version 2>&1 | grep -oE '[0-9]+\.[0-9]+' | head -n 1) bio_row "MAFFT（多序列比对）" 0 "v${cur:-未知}" else bio_row "MAFFT（多序列比对）" 1 fi if command -v iqtree3 >/dev/null 2>&1; then cur=$(iqtree3 --version 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n 1) bio_row "IQ-TREE（系统发育树）" 0 "v${cur:-未知}" else bio_row "IQ-TREE（系统发育树）" 1 fi if command -v R >/dev/null 2>&1; then cur=$(R --version 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n 1) bio_row "R（统计/绘图）" 0 "v${cur:-未知}" else bio_row "R（统计/绘图）" 1 fi if command -v gcc >/dev/null 2>&1 && command -v make >/dev/null 2>&1 && command -v git >/dev/null 2>&1; then bio_row "基础编译环境（gcc/make/git/wget/curl 等）" 0 "gcc v$(gcc -dumpversion 2>/dev/null)" else bio_row "基础编译环境（gcc/make/git/wget/curl 等）" 1 fi echo -e " ${gl_kjlan}[免安装]${gl_bai} ConSurf（蛋白保守性分析）使用 Web Server: https://consurf.tau.ac.cn" if [ ! -x "$bio_env_bin/signalp" ]; then echo -e " ${gl_huang}提示：SignalP 手动安装包请放置于 $bio_work_dir/${gl_bai}" fi echo "----------------------------------------" } bio_install_all() { local fail=0 echo -e "${gl_kjlan}开始一键安装 PspC 生物信息学分析环境……${gl_bai}" echo -e "预计 20-60 分钟（取决于网络）；SignalP 步骤需确认一次学术许可。" echo -e "安装顺序：基础编译环境 → Python 环境 → Biopython → CD-HIT → MAFFT → IQ-TREE → R → SignalP" echo "----------------------------------------" bio_install_buildtools || fail=$((fail+1)) echo "----------------------------------------" bio_install_conda || fail=$((fail+1)) echo "----------------------------------------" bio_install_biopython || fail=$((fail+1)) echo "----------------------------------------" bio_install_cdhit || fail=$((fail+1)) echo "----------------------------------------" bio_install_mafft || fail=$((fail+1)) echo "----------------------------------------" bio_install_iqtree || fail=$((fail+1)) echo "----------------------------------------" bio_install_r || fail=$((fail+1)) echo "----------------------------------------" bio_install_signalp || fail=$((fail+1)) echo "----------------------------------------" if [ "$fail" = "0" ]; then echo -e "${gl_lv}全部组件安装完成！${gl_bai}" else echo -e "${gl_huang}安装结束，其中 $fail 项失败，可从菜单单独重试。${gl_bai}" fi echo -e "${gl_kjlan}环境体检结果：${gl_bai}" bio_check_status } bio_view_log() { if [ ! -f "$bio_log_file" ]; then echo -e "${gl_huang}暂无安装日志（尚未执行过安装）：$bio_log_file${gl_bai}" return 0 fi echo -e "${gl_kjlan}安装日志尾部 100 行${gl_bai}" echo -e "完整日志文件: ${gl_huang}$bio_log_file${gl_bai}" echo "----------------------------------------" tail -n 100 "$bio_log_file" echo "----------------------------------------" echo -e "查看完整日志: ${gl_huang}less -R $bio_log_file${gl_bai}" } bioinfo_menu() { bio_init_paths while true; do clear echo -e "${gl_kjlan}" echo "========================================" echo " 生物信息学分析环境搭建（PspC 清单）" echo "========================================" echo -e "目标系统: Ubuntu 24.04 LTS 环境目录: ${gl_huang}$bio_env_bin${gl_bai}" echo -e "安装日志: ${gl_huang}$bio_log_file${gl_bai}" echo -e "${gl_kjlan}------------------------${gl_bai}" echo -e "${gl_kjlan}1. ${gl_bai}一键安装全部环境（推荐首次使用）" echo -e "${gl_kjlan}------------------------${gl_bai}" echo -e "${gl_kjlan}2. ${gl_bai}Miniconda + Python $bio_python_ver 基础环境" echo -e "${gl_kjlan}3. ${gl_bai}Biopython（FASTA 读取/序列处理）" echo -e "${gl_kjlan}4. ${gl_bai}SignalP $bio_sigp_ver（信号肽预测，需学术许可）" echo -e "${gl_kjlan}5. ${gl_bai}CD-HIT $bio_cdhit_ver（序列去冗余）" echo -e "${gl_kjlan}6. ${gl_bai}MAFFT $bio_mafft_ver（多序列比对）" echo -e "${gl_kjlan}7. ${gl_bai}IQ-TREE $bio_iqtree_ver（系统发育树）" echo -e "${gl_kjlan}8. ${gl_bai}R $bio_r_minver.x+（统计/绘图）" echo -e "${gl_kjlan}9. ${gl_bai}基础编译环境及常用依赖" echo -e "${gl_kjlan}------------------------${gl_bai}" echo -e "${gl_kjlan}10. ${gl_bai}环境体检（查看安装状态与版本）" echo -e "${gl_kjlan}11. ${gl_bai}查看安装日志（排障）" echo -e "${gl_kjlan}------------------------${gl_bai}" echo -e "${gl_kjlan}0. ${gl_bai}返回主菜单" echo -e "${gl_kjlan}------------------------${gl_bai}" read -e -p "请输入你的选择: " choice case $choice in 1) clear; bio_logged "一键安装全部环境" bio_install_all ;; 2) clear; bio_logged "Miniconda + Python $bio_python_ver 环境" bio_install_conda ;; 3) clear; bio_logged "Biopython" bio_install_biopython ;; 4) clear; bio_logged "SignalP $bio_sigp_ver" bio_install_signalp ;; 5) clear; bio_logged "CD-HIT $bio_cdhit_ver" bio_install_cdhit ;; 6) clear; bio_logged "MAFFT $bio_mafft_ver" bio_install_mafft ;; 7) clear; bio_logged "IQ-TREE $bio_iqtree_ver" bio_install_iqtree ;; 8) clear; bio_logged "R $bio_r_minver.x+" bio_install_r ;; 9) clear; bio_logged "基础编译环境及常用依赖" bio_install_buildtools ;; 10) clear; bio_check_status ;; 11) clear; bio_view_log ;; 0) break ;; *) echo "无效的输入!" ;; esac break_end done } # ---------------------------- # 00. 脚本更新 # ---------------------------- kejilion_update() { cd ~ while true; do clear echo "更新日志" echo "------------------------" echo "全部日志: ${dist_base}/kejilion_sh_log.txt" echo "------------------------" curl -s --max-time 15 "${dist_base}/kejilion_sh_log.txt" | tail -n 30 # 只下载文件头部获取版本号，避免下载整个脚本 local sh_v_new=$(curl -s --max-time 15 -r 0-200 "${dist_base}/kejilion.sh" | grep -o 'sh_v="[0-9.]*"' | head -1 | cut -d '"' -f 2) if [ -z "$sh_v_new" ]; then echo -e "${gl_hong}无法获取最新版本信息，请检查网络连接${gl_bai}" elif [ "$sh_v" = "$sh_v_new" ]; then echo -e "${gl_lv}你已经是最新版本！${gl_huang}v$sh_v${gl_bai}" else echo "发现新版本！" echo -e "当前版本 v$sh_v 最新版本 ${gl_huang}v$sh_v_new${gl_bai}" fi local cron_job="kejilion.sh" local existing_cron=$(crontab -l 2>/dev/null | grep -F "$cron_job") if [ -n "$existing_cron" ]; then echo "------------------------" echo -e "${gl_lv}自动更新已开启，每天凌晨2点脚本会自动更新！${gl_bai}" fi echo "------------------------" echo "1. 现在更新 2. 开启自动更新 3. 关闭自动更新" echo "------------------------" echo "0. 返回主菜单" echo "------------------------" read -e -p "请输入你的选择: " choice case "$choice" in 1) clear # 备份当前脚本 cp -f ~/kejilion.sh ~/kejilion.sh.bak 2>/dev/null # 下载到临时文件，校验后再替换 local tmp_file=$(mktemp ~/kejilion_tmp.XXXXXX) if curl -sS --max-time 60 --fail -o "$tmp_file" "${dist_base}/kejilion.sh" && \ [ -s "$tmp_file" ] && \ head -1 "$tmp_file" | grep -q '^#!/bin/bash'; then chmod +x "$tmp_file" mv -f "$tmp_file" ~/kejilion.sh CheckFirstRun_true cp -f ~/kejilion.sh /usr/local/bin/k > /dev/null 2>&1 ln -sf /usr/local/bin/k /usr/bin/k > /dev/null 2>&1 echo -e "${gl_lv}脚本已更新到最新版本！${gl_huang}v$sh_v_new${gl_bai}" else rm -f "$tmp_file" # 恢复备份 if [ -f ~/kejilion.sh.bak ]; then mv -f ~/kejilion.sh.bak ~/kejilion.sh fi echo -e "${gl_hong}更新失败！下载出错或文件校验不通过，已恢复原版本${gl_bai}" fi break_end ~/kejilion.sh exit ;; 2) clear # 自动更新任务：下载到临时文件 → 校验 → 备份 → 替换 → 恢复许可状态 → 部署 k 命令 SH_Update_task="cd ~ && tmp=\$(mktemp ~/kejilion_tmp.XXXXXX) && curl -sS --max-time 60 --fail -o \"\$tmp\" ${dist_base}/kejilion.sh && [ -s \"\$tmp\" ] && head -1 \"\$tmp\" | grep -q '^#!/bin/bash' && cp -f ~/kejilion.sh ~/kejilion.sh.bak 2>/dev/null && chmod +x \"\$tmp\" && mv -f \"\$tmp\" ~/kejilion.sh" # 从旧脚本恢复许可同意状态 SH_Update_task="$SH_Update_task && grep -q 'permission_granted=\"true\"' ~/kejilion.sh.bak 2>/dev/null && sed -i 's/permission_granted=\"false\"/permission_granted=\"true\"/' ~/kejilion.sh" # 部署到 /usr/local/bin/k 和 /usr/bin/k SH_Update_task="$SH_Update_task; cp -f ~/kejilion.sh /usr/local/bin/k 2>/dev/null; ln -sf /usr/local/bin/k /usr/bin/k 2>/dev/null" # 下载失败时清理临时文件 SH_Update_task="$SH_Update_task || rm -f \"\$tmp\" 2>/dev/null" check_crontab_installed (crontab -l | grep -v "kejilion.sh") | crontab - (crontab -l 2>/dev/null; echo "$(shuf -i 0-59 -n 1) 2 * * * bash -c '$SH_Update_task'") | crontab - echo -e "${gl_lv}自动更新已开启，每天凌晨2点脚本会自动更新！${gl_bai}" break_end ;; 3) clear (crontab -l | grep -v "kejilion.sh") | crontab - echo -e "${gl_lv}自动更新已关闭${gl_bai}" break_end ;; *) kejilion_sh ;; esac done } # ---------------------------- # 主菜单 # ---------------------------- kejilion_sh() { while true; do clear echo -e "${gl_kjlan}" echo "========================================" echo -e " 生物信息学脚本工具箱 v$sh_v" echo "========================================" echo -e "命令行输入${gl_huang}k${gl_kjlan}可快速启动脚本${gl_bai}" echo -e "${gl_kjlan}------------------------${gl_bai}" echo -e "${gl_kjlan}1. ${gl_bai}系统信息查询" echo -e "${gl_kjlan}2. ${gl_bai}系统更新" echo -e "${gl_kjlan}3. ${gl_bai}系统清理" echo -e "${gl_kjlan}4. ${gl_bai}生物信息环境搭建" echo -e "${gl_kjlan}------------------------${gl_bai}" echo -e "${gl_kjlan}00. ${gl_bai}脚本更新" echo -e "${gl_kjlan}------------------------${gl_bai}" echo -e "${gl_kjlan}0. ${gl_bai}退出脚本" echo -e "${gl_kjlan}------------------------${gl_bai}" read -e -p "请输入你的选择: " choice case $choice in 1) linux_info ;; 2) clear ; linux_update ;; 3) clear ; linux_clean ;; 4) bioinfo_menu ;; 00) kejilion_update ;; 0) clear ; exit ;; *) echo "无效的输入!" ;; esac break_end done } # ---------------------------- # 自举安装：兼容两种拉取方式 # bash <(curl -sL https://bio-sh.nknpq3nl.icu) 进程替换，源是管道需重新下载落盘 # curl -sL URL -o ~/kejilion.sh && bash ~/kejilion.sh 本地文件，直接复制自身 # ---------------------------- install_self() { local target="$HOME/kejilion.sh" local src="$(readlink -f "${BASH_SOURCE[0]}" 2>/dev/null)" # 进程替换/管道执行时源路径形如 /dev/fd/63，不能作为安装源 case "$src" in /dev/fd/*|/proc/self/fd/*) src="" ;; esac if [ -n "$src" ] && [ -f "$src" ] && [ "$src" != "$target" ]; then cp -f "$src" "$target" elif [ ! -f "$target" ]; then echo -e "${gl_kjlan}正在下载脚本到本地……${gl_bai}" if ! curl -sSfL --max-time 60 "${dist_base}/kejilion.sh" -o "$target"; then echo -e "${gl_hong}安装失败：无法从 ${dist_base} 下载脚本${gl_bai}" return 1 fi fi chmod +x "$target" # 部署 k 快捷命令（需 root 或 /usr/local/bin 可写；失败不阻塞脚本使用） if [ "$(id -u)" -eq 0 ] || [ -w /usr/local/bin ]; then cp -f "$target" /usr/local/bin/k chmod +x /usr/local/bin/k ln -sf /usr/local/bin/k /usr/bin/k 2>/dev/null fi } sed -i '/^alias k=/d' ~/.bashrc > /dev/null 2>&1 sed -i '/^alias k=/d' ~/.profile > /dev/null 2>&1 sed -i '/^alias k=/d' ~/.bash_profile > /dev/null 2>&1 install_self CheckFirstRun_false # ---------------------------- # 入口：无参数进菜单，带参数走精简 k 命令 # ---------------------------- if [ "$#" -eq 0 ]; then # 如果没有参数，运行交互式逻辑 kejilion_sh else # 如果有参数，执行相应函数（仅保留与现有功能兼容的快捷命令） case $1 in install|add|安装) shift install "$@" ;; remove|del|uninstall|卸载) shift remove "$@" ;; update|更新) linux_update ;; clean|清理) linux_clean ;; info) linux_info ;; env|环境) bioinfo_menu ;; *) echo "未知命令: $1" echo "直接运行 k 进入菜单" ;; esac fi