116 lines
3.1 KiB
Bash
116 lines
3.1 KiB
Bash
 
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#!/usr/bin/env bash
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# Check bbav5 project paths, resource links, and core tool startup.
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set -u
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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PROJECT_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
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ENV_FILE="$PROJECT_DIR/.env"
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if [ -f "$ENV_FILE" ]; then
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set -a
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. "$ENV_FILE"
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set +a
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fi
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PROJECT_ROOT="${BBAV5_PROJECT_ROOT:-$PROJECT_DIR}"
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# 镜像标准形态: 无 conda 本体; 当前容器 PATH 即环境 bin(默认当前 shell 的 PATH)。
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CONDA_BASE="${BBAV5_CONDA_BASE:-}"
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DEFAULT_ENV="${BBAV5_DEFAULT_ENV:-}"
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GFPY_ENV="${BBAV5_GFPY_ENV:-}"
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INTERPROSCAN_BIN="${INTERPROSCAN_BIN:-$PROJECT_ROOT/tools/interproscan-5.78-109.0/interproscan.sh}"
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failures=0
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ok() {
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printf '[OK] %s\n' "$1"
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}
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warn() {
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printf '[WARN] %s\n' "$1"
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}
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fail() {
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printf '[FAIL] %s\n' "$1"
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failures=$((failures + 1))
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}
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check_path() {
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local label="$1"
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local path="$2"
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if [ -e "$path" ]; then
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ok "$label exists: $path -> $(readlink -f "$path" 2>/dev/null || printf '%s' "$path")"
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else
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fail "$label missing: $path"
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fi
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}
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check_writable() {
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local label="$1"
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local path="$2"
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if [ -w "$path" ]; then
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ok "$label writable: $path"
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else
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fail "$label not writable: $path"
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fi
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}
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run_check() {
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local label="$1"
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shift
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if "$@" >/tmp/bbav5_env_check.out 2>/tmp/bbav5_env_check.err; then
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ok "$label"
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else
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fail "$label"
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sed 's/^/ stderr: /' /tmp/bbav5_env_check.err | head -5
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fi
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}
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printf 'bbav5 environment check\n'
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printf 'PROJECT_ROOT=%s\n' "$PROJECT_ROOT"
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printf 'CONDA_BASE=%s\n' "$CONDA_BASE"
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if [ "$PROJECT_ROOT" = "$PROJECT_DIR" ]; then
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ok "BBAV5_PROJECT_ROOT matches this project"
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else
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fail "BBAV5_PROJECT_ROOT differs from this project: expected $PROJECT_DIR"
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fi
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check_path ".env" "$ENV_FILE"
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check_path "input" "$PROJECT_ROOT/input"
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check_path "workspace" "$PROJECT_ROOT/workspace"
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check_path "data/hmm/Pfam-A.hmm" "$PROJECT_ROOT/data/hmm/Pfam-A.hmm"
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check_path "data/kegg_new" "$PROJECT_ROOT/data/kegg_new"
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check_path "InterProScan" "$INTERPROSCAN_BIN"
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check_writable "input" "$PROJECT_ROOT/input"
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check_writable "workspace" "$PROJECT_ROOT/workspace"
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# 镜像标准形态: 工具一律 PATH 裸命令(容器内 python -B -m cli.run_xxx 同环境)。
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run_check "hmmsearch starts" hmmsearch -h
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run_check "hmmscan starts" hmmscan -h
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run_check "blastp starts" blastp -version
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run_check "Rscript starts" Rscript -e 'cat("OK\n")'
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# 镜像标准形态: 当前环境 lib 即 /opt/conda/lib(由当前解释器位置推导)。
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lib_dir="$(dirname "$(dirname "$(command -v python || command -v python3)")")/lib"
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if [ ! -d "$lib_dir" ]; then
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warn "python lib dir not found: $lib_dir"
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else
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broken="$(find "$lib_dir" -maxdepth 1 -xtype l -print 2>/dev/null | head -20)"
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if [ -n "$broken" ]; then
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warn "environment has broken top-level library symlinks:"
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printf '%s\n' "$broken" | sed 's/^/ /'
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else
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ok "top-level library symlinks resolve"
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fi
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fi
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if [ "$failures" -eq 0 ]; then
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ok "environment check completed"
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else
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fail "environment check completed with $failures failure(s)"
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fi
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exit "$failures"
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