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tools/bttoxin_digger/README.md

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+# BtToxin_Digger (pixi) reproduction & Docker Image
+
+This repo is a **reproducible runtime environment** for BtToxin_Digger 1.0.10, packaged as a Docker image based on `ghcr.io/prefix-dev/pixi`.
+
+It includes:
+1.  **BtToxin_Digger 1.0.10** (installed via Pixi)
+2.  **BLAST+ 2.16.0** (compatible with v5 databases)
+3.  **Pre-bundled BtToxin Database** (baked into the image)
+
+## License / Citation / Disclaimer
+
+- **BtToxin_Digger** is developed by its original authors; cite the upstream publication if you use it in research.
+- **This repository** only provides an environment wrapper (pixi/docker); it does not modify BtToxin_Digger source code.
+
+## 1. Quick Start with Docker
+
+The easiest way to run this is using the included `docker-compose.yml` or the global project configuration.
+
+### Build the Image
+
+```bash
+# In this directory
+docker compose build
+```
+
+### Run Analysis
+
+Place your input `.fna` files in `examples/inputs` (or mount your own directory), then run:
+
+```bash
+# Run help
+docker compose run --rm digger-repro pixi run BtToxin_Digger --help
+
+# Run analysis on a specific file
+# Note: Input path must match the internal mount point (/app/jobs)
+docker compose run --rm digger-repro pixi run BtToxin_Digger \
+  --SeqPath /app/jobs \
+  --Scaf_suffix .fna \
+  --threads 4
+```
+
+### Directory Mounting
+
+- `/app/jobs`: Mount your input sequence files here.
+- `/app/data`: Mount your desired output directory here (if using absolute paths in arguments).
+
+## 2. Docker Image Construction
+
+The image is built using `docker/Dockerfile`.
+
+### Base Image
+Uses `ghcr.io/prefix-dev/pixi:latest` to ensure a consistent conda-compatible environment.
+
+### Database Integration
+The external database (`external_dbs/bt_toxin`) is **copied into the image** during build time.
+Target location: `/app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin`
+
+This replaces the default database shipped with the bioconda package, ensuring:
+1.  Latest toxin definitions are used.
+2.  BLAST v5 indices are compatible with the installed BLAST+ 2.16.0.
+
+### Environment Definition (`pixi.toml`)
+- `bttoxin_digger = "==1.0.10"`
+- `perl = "==5.26.2"` (Legacy requirement)
+- `blast = "==2.16.0"` (Upgraded for v5 DB support)
+- `channel-priority = "disabled"`
+
+## 3. Development / Manual Usage
+
+If you want to run without Docker using local Pixi:
+
+```bash
+# Install environment
+pixi install
+
+# Link the database (required manually if not using Docker)
+# The Dockerfile does this automatically by copying files.
+ENV_BIN=.pixi/envs/default/bin
+rm -rf "$ENV_BIN/BTTCMP_db/bt_toxin"
+ln -sfn $(pwd)/external_dbs/bt_toxin "$ENV_BIN/BTTCMP_db/bt_toxin"
+
+# Run
+pixi run BtToxin_Digger --help
+```
+
+## 4. Repository Layout
+
+```
+.
+├── docker/
+│   └── Dockerfile          # Docker build definition
+├── docker-compose.yml      # Local test orchestration
+├── external_dbs/           # Database source (copied into image)
+│   └── bt_toxin/           # The actual database files
+├── pixi.toml               # Environment dependencies
+├── pixi.lock               # Exact version lock
+└── examples/               # Test inputs and outputs
+```
+
+## 5. Updating the Database (Important for Future Updates)
+
+The database consists of two parts in `external_dbs/bt_toxin`:
+1.  **`seq/` Directory**: Contains the raw FASTA sequence files (e.g., `bt_toxin20251104.fas`).
+2.  **`db/` Directory**: Contains the BLAST indices (`.phr`, `.pin`, `.psq`) generated from the sequences.
+
+**Relationship**: The files in `db/` are **generated from** the FASTA files in `seq/` using `makeblastdb`. The filename of the source FASTA (e.g., `bt_toxin20251104.fas`) is embedded in the `db` files metadata.
+
+### How to Update (e.g., for 2026/2027 data)
+
+If a new database version is released (e.g., from https://github.com/liaochenlanruo/BtToxin_Digger), follow these steps:
+
+1.  **Download New Sequences**:
+    Place the new FASTA file (e.g., `bt_toxin2026xxxx.fas`) into `external_dbs/bt_toxin/seq/`.
+
+2.  **Generate New Indices (Critical Step)**:
+    You must regenerate the indices in `external_dbs/bt_toxin/db/`. You can use a temporary container or local BLAST+ to do this.
+
+    ```bash
+    # Example using the local pixi environment (if installed)
+    # Or use a container with blast installed
+    makeblastdb \
+        -in external_dbs/bt_toxin/seq/bt_toxin2026xxxx.fas \
+        -dbtype prot \
+        -out external_dbs/bt_toxin/db/bt_toxin \
+        -parse_seqids
+    ```
+
+    *Note: The `-out` parameter must end with `bt_toxin` to match what the tool expects.*
+
+3.  **Rebuild Docker Image**:
+    The Dockerfile copies `external_dbs/bt_toxin` into the image. You must rebuild it to include the changes.
+
+    ```bash
+    docker compose build --no-cache
+    ```
+
+4.  **Verify**:
+    Check the database version inside the new container:
+    ```bash
+    docker compose run --rm digger-repro pixi run blastdbcmd -db /app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin/db/bt_toxin -info
+    ```