feat: migrate from Docker to pixi for BtToxin_Digger execution

- Add pixi.toml with digger and pipeline environments
- Implement PixiRunner class replacing DockerContainerManager
- Add run_digger_stage.py for standalone digger execution
- Update run_single_fna_pipeline.py to use PixiRunner
- Remove docker dependency from pyproject.toml
- Delete docker_client.py (no longer needed)

BREAKING CHANGE: Docker is no longer required. Use 'pixi install' instead.

scripts/run_single_fna_pipeline.py

@@ -3,20 +3,20 @@
 
 - Input: one .fna file (nucleotide scaffold)
 - Steps:
-  1) Stage this single file, run BtToxin_Digger via DockerContainerManager
-  2) Run Shotter scoring on Digger's All_Toxins.txt
-  3) Render heatmaps + paper-style report
+  1) Stage this single file, run BtToxin_Digger via PixiRunner (pixi environment)
+  2) Run Shotter scoring on Digger's All_Toxins.txt via pixi run -e pipeline
+  3) Render heatmaps + paper-style report via pixi run -e pipeline
   4) Organize outputs under one root folder:
      <out_root>/
-       ├─ digger/   (container outputs)
+       ├─ digger/   (pixi digger env outputs)
        ├─ shotter/  (Shotter TSV/JSON + plots + report)
        └─ pipeline_results.tar.gz (bundle)
 
 Notes
-- Digger is executed in a container (root in container); files may be owned by root on host.
-  We write everything into <out_root>/digger to keep permissions/locality predictable.
+- Digger is executed in the pixi 'digger' environment with bioconda dependencies.
+- Shotter and plotting are executed in the pixi 'pipeline' environment with Python dependencies.
 - This script exposes CLI flags for Shotter filters to allow strict/loose runs.
-- 默认使用 external_dbs/bt_toxin 作为外部数据库（若存在），覆盖容器内置旧库。
+- 默认使用 external_dbs/bt_toxin 作为外部数据库（若存在）。
 
 Example
   python scripts/run_single_fna_pipeline.py \\
@@ -30,6 +30,9 @@ Example
   python scripts/run_single_fna_pipeline.py \\
     --fna tests/test_data/HAN055.fna \\
     --bttoxin_db_dir /path/to/custom/bt_toxin
+
+  # 使用 pixi 任务运行
+  pixi run pipeline --fna tests/test_data/HAN055.fna
 """
 from __future__ import annotations
 
@@ -40,11 +43,10 @@ import subprocess
 import sys
 import tarfile
 from pathlib import Path
-from typing import Dict, Any
+from typing import Dict, Any, List
 
-# import DockerContainerManager from backend
-sys.path.append(str(Path(__file__).resolve().parents[1] / "backend"))
-from app.utils.docker_client import DockerContainerManager  # type: ignore
+# Import PixiRunner and command builders from scripts
+from pixi_runner import PixiRunner, build_shotter_command, build_plot_command
 
 
 def _shell(cmd: list[str]) -> subprocess.CompletedProcess:
@@ -72,20 +74,28 @@ def run_single_fna_pipeline(
     fna_path: Path,
     out_root: Path,
     toxicity_csv: Path = Path("Data/toxicity-data.csv"),
-    image: str = "quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0",
-    platform: str = "linux/amd64",
     min_identity: float = 0.0,
     min_coverage: float = 0.0,
     allow_unknown_families: bool = True,
     require_index_hit: bool = False,
     lang: str = "zh",
     bttoxin_db_dir: Path | None = None,
+    threads: int = 4,
 ) -> Dict[str, Any]:
-    """运行单个 fna 文件的完整 pipeline。
+    """运行单个 fna 文件的完整 pipeline（使用 pixi 环境）。
 
     Args:
+        fna_path: 输入 .fna 文件路径
+        out_root: 输出根目录
+        toxicity_csv: 毒性数据 CSV 文件路径
+        min_identity: 最小 identity 阈值
+        min_coverage: 最小 coverage 阈值
+        allow_unknown_families: 是否允许未知家族
+        require_index_hit: 是否要求索引命中
+        lang: 报告语言 (zh/en)
         bttoxin_db_dir: 外部 bt_toxin 数据库目录。若为 None，则自动检测
                        项目根目录下的 external_dbs/bt_toxin。
+        threads: 线程数
     """
     fna_path = fna_path.resolve()
     out_root = out_root.resolve()
@@ -98,7 +108,7 @@ def run_single_fna_pipeline(
             bttoxin_db_dir = default_db
             print(f"[pipeline] 使用外部数据库: {bttoxin_db_dir}")
         else:
-            print("[pipeline] 未找到外部数据库，将使用容器内置数据库（可能较旧）")
+            print("[pipeline] 未找到外部数据库，将使用 pixi 环境内置数据库")
 
     digger_dir = out_root / "digger"
     shotter_dir = out_root / "shotter"
@@ -111,15 +121,15 @@ def run_single_fna_pipeline(
     staged_fna = stage_dir / fna_path.name
     shutil.copy2(fna_path, staged_fna)
 
-    # 1) Run BtToxin_Digger via DockerContainerManager
-    mgr = DockerContainerManager(image=image, platform=platform)
-    result = mgr.run_bttoxin_digger(
+    # 1) Run BtToxin_Digger via PixiRunner (pixi digger environment)
+    runner = PixiRunner(env_name="digger")
+    result = runner.run_bttoxin_digger(
         input_dir=stage_dir,
         output_dir=digger_dir,
         log_dir=logs_dir,
         sequence_type="nucl",
         scaf_suffix=fna_path.suffix or ".fna",
-        threads=4,
+        threads=threads,
         bttoxin_db_dir=bttoxin_db_dir,
     )
     if not result.get("success"):
@@ -135,27 +145,22 @@ def run_single_fna_pipeline(
     if not all_toxins.exists():
         return {"ok": False, "stage": "digger", "error": f"Missing All_Toxins.txt at {all_toxins}"}
 
-    # 2) Run Shotter scoring
+    # 2) Run Shotter scoring via pixi run -e pipeline
     shotter_dir.mkdir(parents=True, exist_ok=True)
-    py = sys.executable
-    shoter_cmd: list[str] = [
-        py,
-        str(Path(__file__).resolve().parents[0] / "bttoxin_shoter.py"),
-        "--toxicity_csv",
-        str(toxicity_csv),
-        "--all_toxins",
-        str(all_toxins),
-        "--output_dir",
-        str(shotter_dir),
-    ]
-    if min_identity and min_identity > 0:
-        shoter_cmd += ["--min_identity", str(min_identity)]
-    if min_coverage and min_coverage > 0:
-        shoter_cmd += ["--min_coverage", str(min_coverage)]
-    if not allow_unknown_families:
-        shoter_cmd += ["--disallow_unknown_families"]
-    if require_index_hit:
-        shoter_cmd += ["--require_index_hit"]
+    scripts_dir = Path(__file__).resolve().parents[0]
+    pixi_project_dir = Path(__file__).resolve().parents[1]
+    
+    shoter_cmd = build_shotter_command(
+        pixi_project_dir=pixi_project_dir,
+        script_path=scripts_dir / "bttoxin_shoter.py",
+        toxicity_csv=toxicity_csv,
+        all_toxins=all_toxins,
+        output_dir=shotter_dir,
+        min_identity=min_identity,
+        min_coverage=min_coverage,
+        allow_unknown_families=allow_unknown_families,
+        require_index_hit=require_index_hit,
+    )
 
     r1 = _shell(shoter_cmd)
     if r1.returncode != 0:
@@ -165,27 +170,20 @@ def run_single_fna_pipeline(
     toxin_support = shotter_dir / "toxin_support.tsv"
     species_scores = shotter_dir / "strain_target_species_scores.tsv"
 
-    # 3) Plot & report
+    # 3) Plot & report via pixi run -e pipeline
     strain_for_plot = _read_first_strain(strain_scores)
-    plot_cmd: list[str] = [
-        py,
-        str(Path(__file__).resolve().parents[0] / "plot_shotter.py"),
-        "--strain_scores",
-        str(strain_scores),
-        "--toxin_support",
-        str(toxin_support),
-        "--species_scores",
-        str(species_scores),
-        "--out_dir",
-        str(shotter_dir),
-        "--merge_unresolved",
-        "--report_mode",
-        "paper",
-        "--lang",
-        lang,
-    ]
-    if strain_for_plot:
-        plot_cmd += ["--per_hit_strain", strain_for_plot]
+    plot_cmd = build_plot_command(
+        pixi_project_dir=pixi_project_dir,
+        script_path=scripts_dir / "plot_shotter.py",
+        strain_scores=strain_scores,
+        toxin_support=toxin_support,
+        species_scores=species_scores,
+        out_dir=shotter_dir,
+        merge_unresolved=True,
+        report_mode="paper",
+        lang=lang,
+        per_hit_strain=strain_for_plot if strain_for_plot else None,
+    )
 
     r2 = _shell(plot_cmd)
     if r2.returncode != 0:
@@ -209,12 +207,10 @@ def run_single_fna_pipeline(
 
 
 def main() -> int:
-    ap = argparse.ArgumentParser(description="Run single-fna Digger -> Shotter pipeline")
+    ap = argparse.ArgumentParser(description="Run single-fna Digger -> Shotter pipeline (pixi-based)")
     ap.add_argument("--fna", type=Path, required=True, help="Path to a single .fna file")
     ap.add_argument("--toxicity_csv", type=Path, default=Path("Data/toxicity-data.csv"))
     ap.add_argument("--out_root", type=Path, default=Path("runs/single_run"))
-    ap.add_argument("--image", type=str, default="quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0")
-    ap.add_argument("--platform", type=str, default="linux/amd64")
     ap.add_argument("--min_identity", type=float, default=0.0)
     ap.add_argument("--min_coverage", type=float, default=0.0)
     ap.add_argument("--disallow_unknown_families", action="store_true", default=False)
@@ -222,6 +218,7 @@ def main() -> int:
     ap.add_argument("--lang", type=str, choices=["zh", "en"], default="zh")
     ap.add_argument("--bttoxin_db_dir", type=Path, default=None,
                     help="外部 bt_toxin 数据库目录路径（默认自动检测 external_dbs/bt_toxin）")
+    ap.add_argument("--threads", type=int, default=4, help="线程数")
     args = ap.parse_args()
 
     # derive per-run default out_root using file stem
@@ -233,14 +230,13 @@ def main() -> int:
         fna_path=args.fna,
         out_root=args.out_root,
         toxicity_csv=args.toxicity_csv,
-        image=args.image,
-        platform=args.platform,
         min_identity=args.min_identity,
         min_coverage=args.min_coverage,
         allow_unknown_families=not args.disallow_unknown_families,
         require_index_hit=args.require_index_hit,
         lang=args.lang,
         bttoxin_db_dir=args.bttoxin_db_dir,
+        threads=args.threads,
     )
 
     if not res.get("ok"):