166af50219
- Moved bttoxin_digger_v5_repro to tools/reproduction/bttoxin_digger - Updated docker-compose.yml to point to the new location - This declutters the root directory while preserving the reproduction environment
142 lines
4.9 KiB
Markdown
142 lines
4.9 KiB
Markdown
# BtToxin_Digger (pixi) reproduction & Docker Image
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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`.
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It includes:
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1. **BtToxin_Digger 1.0.10** (installed via Pixi)
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2. **BLAST+ 2.16.0** (compatible with v5 databases)
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3. **Pre-bundled BtToxin Database** (baked into the image)
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## License / Citation / Disclaimer
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- **BtToxin_Digger** is developed by its original authors; cite the upstream publication if you use it in research.
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- **This repository** only provides an environment wrapper (pixi/docker); it does not modify BtToxin_Digger source code.
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## 1. Quick Start with Docker
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The easiest way to run this is using the included `docker-compose.yml` or the global project configuration.
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### Build the Image
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```bash
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# In this directory
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docker compose build
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```
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### Run Analysis
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Place your input `.fna` files in `examples/inputs` (or mount your own directory), then run:
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```bash
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# Run help
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docker compose run --rm digger-repro pixi run BtToxin_Digger --help
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# Run analysis on a specific file
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# Note: Input path must match the internal mount point (/app/jobs)
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docker compose run --rm digger-repro pixi run BtToxin_Digger \
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--SeqPath /app/jobs \
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--Scaf_suffix .fna \
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--threads 4
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```
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### Directory Mounting
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- `/app/jobs`: Mount your input sequence files here.
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- `/app/data`: Mount your desired output directory here (if using absolute paths in arguments).
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## 2. Docker Image Construction
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The image is built using `docker/Dockerfile`.
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### Base Image
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Uses `ghcr.io/prefix-dev/pixi:latest` to ensure a consistent conda-compatible environment.
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### Database Integration
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The external database (`external_dbs/bt_toxin`) is **copied into the image** during build time.
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Target location: `/app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin`
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This replaces the default database shipped with the bioconda package, ensuring:
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1. Latest toxin definitions are used.
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2. BLAST v5 indices are compatible with the installed BLAST+ 2.16.0.
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### Environment Definition (`pixi.toml`)
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- `bttoxin_digger = "==1.0.10"`
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- `perl = "==5.26.2"` (Legacy requirement)
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- `blast = "==2.16.0"` (Upgraded for v5 DB support)
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- `channel-priority = "disabled"`
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## 3. Development / Manual Usage
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If you want to run without Docker using local Pixi:
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```bash
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# Install environment
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pixi install
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# Link the database (required manually if not using Docker)
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# The Dockerfile does this automatically by copying files.
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ENV_BIN=.pixi/envs/default/bin
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rm -rf "$ENV_BIN/BTTCMP_db/bt_toxin"
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ln -sfn $(pwd)/external_dbs/bt_toxin "$ENV_BIN/BTTCMP_db/bt_toxin"
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# Run
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pixi run BtToxin_Digger --help
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```
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## 4. Repository Layout
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```
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├── docker/
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│ └── Dockerfile # Docker build definition
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├── docker-compose.yml # Local test orchestration
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├── external_dbs/ # Database source (copied into image)
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│ └── bt_toxin/ # The actual database files
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├── pixi.toml # Environment dependencies
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├── pixi.lock # Exact version lock
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└── examples/ # Test inputs and outputs
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```
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## 5. Updating the Database (Important for Future Updates)
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The database consists of two parts in `external_dbs/bt_toxin`:
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1. **`seq/` Directory**: Contains the raw FASTA sequence files (e.g., `bt_toxin20251104.fas`).
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2. **`db/` Directory**: Contains the BLAST indices (`.phr`, `.pin`, `.psq`) generated from the sequences.
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**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.
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### How to Update (e.g., for 2026/2027 data)
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If a new database version is released (e.g., from https://github.com/liaochenlanruo/BtToxin_Digger), follow these steps:
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1. **Download New Sequences**:
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Place the new FASTA file (e.g., `bt_toxin2026xxxx.fas`) into `external_dbs/bt_toxin/seq/`.
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2. **Generate New Indices (Critical Step)**:
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You must regenerate the indices in `external_dbs/bt_toxin/db/`. You can use a temporary container or local BLAST+ to do this.
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```bash
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# Example using the local pixi environment (if installed)
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# Or use a container with blast installed
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makeblastdb \
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-in external_dbs/bt_toxin/seq/bt_toxin2026xxxx.fas \
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-dbtype prot \
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-out external_dbs/bt_toxin/db/bt_toxin \
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-parse_seqids
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```
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*Note: The `-out` parameter must end with `bt_toxin` to match what the tool expects.*
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3. **Rebuild Docker Image**:
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The Dockerfile copies `external_dbs/bt_toxin` into the image. You must rebuild it to include the changes.
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```bash
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docker compose build --no-cache
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```
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4. **Verify**:
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Check the database version inside the new container:
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```bash
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docker compose run --rm digger-repro pixi run blastdbcmd -db /app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin/db/bt_toxin -info
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```
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