adminandClaude Fable 5
dd0cd01e61
按 playbook 方法补做台账 9-25 号共 16 个环境镜像(工程收尾): - 11 个 conda env + 4 个 biolabx(mamba/micromamba) + pymol-env(conda 环境) - 豁免 3 个: AI_env(12K 空壳)/r_de(残壳)/miniconda3 base(conda 本体违红线) - 新增坑位 17-21: conda-pack -n 需 PATH/pip 覆盖检测/dest-prefix 路线 (无 python 环境)/pip shebang 源前缀/conda-unpack 残留 - build_envs.sh: 非内核镜像构建入口; extra-envs/: 16 个 Dockerfile - 验证: 16/16 过 §6 清单+加强断言(无 conda-unpack/无源前缀 shebang) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
67 lines
2.3 KiB
Bash
Executable File
67 lines
2.3 KiB
Bash
Executable File
#!/usr/bin/env bash
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# build_envs.sh —— 非内核环境镜像构建(plantai-env-* 系列, playbook §8 台账 9-24 号)
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# 方法: docs/bioflow_image_build_playbook.md; 与 build_all.sh 同级的第二个构建入口。
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# 用法: build_envs.sh <comma-list|all> [pack-dir]
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# pack-dir: 存放 conda-pack 产物 <env>.tar.gz 的目录; 默认 bioflow-image-build。
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set -euo pipefail
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TARGET="${1:-all}"
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PACK_DIR="${2:-/home/xzq/5090/teamWorkspace/zh/bioflow-image-build}"
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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DF_DIR="$SCRIPT_DIR/extra-envs"
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TAG="${PLANTAI_ENV_TAG:-20260906}"
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# 镜像名 -> 源 tar(构建顺序: 大 tar 先行, I/O 平摊)
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declare -A TARS=(
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[minerupy312]=minerupy312.tar.gz
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[at-sc]=at_sc.tar.gz
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[snpeff]=snpeff.tar.gz
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[plantai-bff]=plantai-bff.tar.gz
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[rice-download]=rice_download.tar.gz
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[rice-rna]=rice_rna-dp.tar.gz
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[beagle54]=beagle54-dp.tar.gz
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[bioinfo]=bioinfo.tar.gz
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[testpy311]=testpy311.tar.gz
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[ani]=ani-dp.tar.gz
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[vcflinshi]=vcflinshi-dp.tar.gz
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[biolabx-assembly]=biolabx-assembly.tar.gz
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[biolabx-bioinfo]=biolabx-bioinfo-missing.tar.gz
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[biolabx-smoke-tools]=biolabx-smoke-tools.tar.gz
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[biolabx-variant-tools]=biolabx-variant-tools.tar.gz
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[pymol-env]=pymol-env.tar.gz
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)
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ORDER=(minerupy312 at-sc snpeff plantai-bff rice-download rice-rna beagle54 bioinfo \
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testpy311 ani vcflinshi biolabx-assembly biolabx-bioinfo biolabx-smoke-tools \
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biolabx-variant-tools pymol-env)
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build_one() {
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local img="$1"
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local tarf="${TARS[$img]}"
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[[ -f "$PACK_DIR/$tarf" ]] || { echo "[FAIL] missing pack artifact: $tarf" >&2; return 2; }
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# 构建上下文: pack-dir 下 stage(硬链接 tar, 同文件系统; 非内核镜像无源码)
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local stage
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stage="$(mktemp -d "$PACK_DIR/.buildenv.XXXXXX")"
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ln "$PACK_DIR/$tarf" "$stage/$tarf"
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echo "[BUILD] plantai-env-$img ($tarf)"
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docker build \
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--build-arg BASE_IMAGE="ubuntu:24.04" \
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--build-arg ENV_TAR="$tarf" \
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-f "$DF_DIR/Dockerfile.plantai-env-$img" \
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-t "plantai-env-$img:$TAG" \
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"$stage"
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rm -rf "$stage"
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echo "[OK] plantai-env-$img"
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}
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if [[ "$TARGET" == "all" ]]; then
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for img in "${ORDER[@]}"; do
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build_one "$img"
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done
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else
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IFS=, read -ra IMGS <<< "$TARGET"
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for img in "${IMGS[@]}"; do
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[[ -n "${TARS[$img]:-}" ]] || { echo "unknown image: $img" >&2; exit 2; }
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build_one "$img"
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done
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fi
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