Add Dorado 0.8.0 Dockerfile and README

dorado/0.8.0/Dockerfile

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+# Use NVIDIA CUDA image as the base image
+FROM nvidia/cuda:12.2.0-devel-ubuntu20.04 AS app
+
+ARG DORADO_VER=0.8.0
+
+# Metadata
+LABEL base.image="nvidia/cuda:12.2.0-devel-ubuntu20.04"
+LABEL dockerfile.version="1"
+LABEL software="dorado ${DORADO_VER}"
+LABEL software.version="${DORADO_VER}"
+LABEL description="A tool for basecalling Fast5/Pod5 files from Oxford Nanopore sequencing"
+LABEL website="https://github.com/nanoporetech/dorado"
+LABEL license="https://github.com/nanoporetech/dorado/blob/master/LICENSE"
+LABEL original.website="https://nanoporetech.github.io/dorado/"
+LABEL maintainer="Fraser Combe"
+LABEL maintainer.email="[email protected]"
+
+# Set working directory
+WORKDIR /usr/src/app
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    wget
+
+# Download and extract Dorado package
+RUN wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-${DORADO_VER}-linux-x64.tar.gz \
+    && tar -xzvf dorado-${DORADO_VER}-linux-x64.tar.gz -C /opt \
+    && rm dorado-${DORADO_VER}-linux-x64.tar.gz
+
+# Set environment variables for Dorado binary
+ENV PATH="/opt/dorado-${DORADO_VER}-linux-x64/bin:${PATH}"
+
+# Download basecalling models
+RUN mkdir /dorado_models && \
+    cd /dorado_models && \
+    dorado download --model all
+
+# Download the specific Pod5 test file
+RUN wget -O /usr/src/app/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 \
+  https://github.com/nanoporetech/dorado/raw/release-v0.7/tests/data/pod5/dna_r10.4.1_e8.2_260bps/\
+dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5
+
+# Default command
+CMD ["dorado"]
+
+# -----------------------------
+# Test Stage
+# -----------------------------
+FROM app AS test
+
+# Set working directory
+WORKDIR /usr/src/app
+
+# Run test command (using CPU mode)
+RUN dorado basecaller \
+    --device cpu \
+    /dorado_models/[email protected] \
+    dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 \
+    --emit-moves --max-reads 10 > basecalled.sam
+
+# Verify the output file exists and is not empty
+RUN test -s basecalled.sam

dorado/0.8.0/README.md

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+# Dorado Docker Image
+
+This Dockerfile sets up an environment for running **Dorado**, a tool for basecalling Fast5/Pod5 files from Oxford Nanopore sequencing.
+
+## Table of Contents
+
+- [Introduction](#introduction)
+- [Requirements](#requirements)
+- [Building the Docker Image](#building-the-docker-image)
+- [Running the Docker Container](#running-the-docker-container)
+- [Testing the Docker Image](#testing-the-docker-image)
+- [Basecalling Test](#basecalling-test)
+- [Verifying the Output](#verifying-the-output)
+- [Additional Notes](#additional-notes)
+- [License](#license)
+
+## Introduction
+
+This Docker image includes:
+
+- **Dorado**: Version **0.8.0**, a tool for basecalling Oxford Nanopore sequencing data.
+- **NVIDIA CUDA**: Version **12.2.0**, for GPU acceleration (requires NVIDIA GPU).
+- **Pre-downloaded basecalling models**: All models are downloaded during the build.
+- **Sample Pod5 test file**: Included for testing the basecalling process.
+
+## Requirements
+
+- **Docker**: Installed on your system.
+- **NVIDIA GPU and Drivers**: Installed and configured.
+- **NVIDIA Container Toolkit**: To enable GPU support in Docker containers.
+
+## Building the Docker Image
+
+ **Build the Docker image** using the following command:
+
+   ```bash
+   docker build -t dorado-image .
+   ```
+
+## Running the Docker Container
+
+To run the Dorado tool within the Docker container, use the following command:
+
+```bash
+docker run --gpus all -it dorado-image dorado --help
+```
+
+This command will display the help information for Dorado, confirming that it's installed correctly.
+
+## Testing the Docker Image
+
+To test that Dorado is working correctly, perform a basecalling operation using the provided sample Pod5 file and basecalling models.
+
+### Basecalling Test
+
+Run the following command:
+
+```bash
+docker run --gpus all -v $(pwd):/usr/src/app -it dorado-image bash -c "\
+  dorado basecaller /dorado_models/[email protected] \
+  /usr/src/app/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 \
+  --emit-moves > /usr/src/app/basecalled.sam"
+```
+
+**Explanation:**
+
+- `--gpus all`: Enables GPU support.
+- `-v $(pwd):/usr/src/app`: Mounts the current directory to `/usr/src/app` inside the container.
+- `bash -c "...":` Runs the basecalling command inside the container.
+- `> /usr/src/app/basecalled.sam`: Redirects the output to `basecalled.sam` in your current directory.
+
+### Verifying the Output
+
+Check the output file to ensure basecalling was successful:
+
+```bash
+less basecalled.sam
+```
+
+You should see SAM-formatted basecalling results.
+
+## Additional Notes
+
+- **Basecalling Models**: All models are downloaded to `/dorado_models` during the build process.
+- **Sample Data**: The sample Pod5 file is downloaded to `/usr/src/app` during the build.
+- **Internal Testing**: An internal test stage is included in the Dockerfile to verify installation.
+
+## License
+
+Dorado is licensed under [Oxford Nanopore Technologies' License](https://github.com/nanoporetech/dorado/blob/master/LICENSE).
+
+
+---
+
+**Note**: Please ensure that you have the necessary NVIDIA drivers and the NVIDIA Container Toolkit installed to utilize GPU acceleration.
+
+---