fix(bioflow): 内核树运行时挂载——非 gf 阶段镜像缺 cli 模块

- 8 个阶段镜像中仅 bioflow-gf 内置 /bioflow-kernel,其余 7 个
  (rnaseq/wgs/gfpy/rnar/rde/pan/interproscan) 执行时 No module named cli
- 服务端统一 -v kernel_dir:/bioflow-kernel:ro + -w /bioflow-kernel,
  全部镜像可用,免重建 7 个镜像
- config 新增 kernel_dir/container_kernel_dir(env 可覆盖)
- 337 用例全绿

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

bioflow_service/app/config.py

@@ -35,6 +35,10 @@ class Settings(BaseSettings):
 
     # ---- 阶段→镜像映射（A1 交付物，仓库内 bioflow_kernel/stage_image_map.json）----
     image_map_path: str = "bioflow_kernel/stage_image_map.json"
+    # 内核树：运行时只读挂载进执行容器（-v kernel:/bioflow-kernel:ro + -w）
+    # 除 bioflow-gf 外其余镜像未内置内核，挂载后全部阶段镜像统一可用
+    kernel_dir: str = "bioflow_kernel"
+    container_kernel_dir: str = "/bioflow-kernel"
 
     # ---- 数据与任务目录 ----
     data_root: str = "bioflow_data"          # 生信数据根（hmm/rag_db 等，只读挂载进容器）
@@ -125,6 +129,10 @@ class Settings(BaseSettings):
     def data_root_abs(self) -> str:
         return _resolve_root(self.data_root)
 
+    @property
+    def kernel_dir_abs(self) -> str:
+        return _resolve_root(self.kernel_dir)
+
     @property
     def jobs_dir_abs(self) -> str:
         return _resolve_root(self.jobs_dir)

bioflow_service/app/services/bioflow/kernel.py

@@ -72,6 +72,8 @@ class KernelConfig:
     cpu_allow: str = "4,8,16,32"
     memory_allow: str = "16g,32g,64g"
     extra_mounts: list[str] = field(default_factory=list)  # 登记路径只读挂载(src==dst)
+    kernel_dir: str = ""                # 内核树宿主路径(运行时挂载进容器)
+    container_kernel_dir: str = "/bioflow-kernel"  # 容器内内核树路径
 
 
 class Kernel:
@@ -145,6 +147,10 @@ class Kernel:
         # 登记路径只读挂载（src==dst，容器内原路径直接可见；登记时已过黑名单）
         for m in (extra_mounts or self.cfg.extra_mounts):
             cmd += ["-v", f"{m}:{m}:ro"]
+        # 内核树运行时挂载（除 bioflow-gf 外其余镜像未内置内核，统一走挂载）
+        if self.cfg.kernel_dir:
+            cmd += ["-v", f"{self.cfg.kernel_dir}:{self.cfg.container_kernel_dir}:ro"]
+            cmd += ["-w", self.cfg.container_kernel_dir]
         eff_cpu = cpu or str(params.get("cpu") or "")
         eff_memory = memory or str(params.get("memory") or "")
         cmd += ["--cpus", self._safe_cpu(eff_cpu or self.cfg.default_cpus)]
@@ -286,6 +292,8 @@ def _default_kernel_config() -> KernelConfig:
         stage_timeout_sec=s.stage_timeout_sec,
         log_tail_lines=s.log_tail_lines,
         bba_env=s.bba_env,
+        kernel_dir=s.kernel_dir_abs,
+        container_kernel_dir=s.container_kernel_dir,
     )
 
 

bioflow_service/tests/test_kernel.py

@@ -75,6 +75,20 @@ def test_build_command_extra_mounts(kernel, tmp_path):
         assert f"{m}:{m}:ro" in cmd
 
 
+def test_build_command_kernel_dir_mount(tmp_path):
+    """内核树运行时挂载：-v kernel:/bioflow-kernel:ro + -w /bioflow-kernel。"""
+    from app.services.bioflow.kernel import Kernel, KernelConfig, ImageMap
+    cfg = KernelConfig(host_uid=1234, kernel_dir=str(tmp_path / "kernel"),
+                       container_kernel_dir="/bioflow-kernel",
+                       data_root=str(tmp_path / "data"))
+    img = ImageMap(images={"gf": {"docker_tag": "bioflow-gf"}},
+                   stages={"identify": {"image": "gf", "module": "cli.run_identify"}})
+    k = Kernel(img, cfg)
+    cmd = k.build_command("identify", tmp_path / "in", tmp_path / "ws")
+    assert f"{tmp_path}/kernel:/bioflow-kernel:ro" in cmd
+    assert "-w" in cmd and "/bioflow-kernel" in cmd
+
+
 def test_build_command_params(kernel, tmp_path):
     cmd = kernel.build_command("identify", tmp_path / "in", tmp_path / "ws",
                                {"prefix": "Ft.SPL", "required_pfams": "PF03110",