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* Add Dorado 0.8.0 Dockerfile and README * PR changes dorado * Update Program_Licenses.md * Update README.md * clarified section on test POD5 file --------- Co-authored-by: Curtis Kapsak <[email protected]>
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| # Use NVIDIA CUDA image as the base image | ||
| FROM nvidia/cuda:12.2.0-devel-ubuntu20.04 AS app | ||
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| ARG DORADO_VER=0.8.0 | ||
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| # 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]" | ||
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| # Set working directory | ||
| WORKDIR /usr/src/app | ||
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| # Install dependencies | ||
| RUN apt-get update && \ | ||
| apt-get install -y --no-install-recommends wget ca-certificates && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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| # 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-${DORADO_VER}-linux-x64.tar.gz | ||
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| # Set environment variables for Dorado binary | ||
| ENV PATH="/opt/dorado-${DORADO_VER}-linux-x64/bin:${PATH}" | ||
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| # Download basecalling models | ||
| RUN mkdir /dorado_models && \ | ||
| cd /dorado_models && \ | ||
| dorado download --model all | ||
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| # Default command | ||
| CMD ["dorado"] | ||
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| # ----------------------------- | ||
| # Test Stage | ||
| # ----------------------------- | ||
| FROM app AS test | ||
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| # 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 | ||
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| # Set working directory | ||
| WORKDIR /usr/src/app | ||
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| # 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 | ||
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| # Verify the output file exists and is not empty | ||
| RUN test -s basecalled.sam |
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| # Dorado Docker Image | ||
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| This Dockerfile sets up an environment for running **Dorado**, a tool for basecalling Fast5/Pod5 files from Oxford Nanopore sequencing. | ||
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| ## Table of Contents | ||
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| - [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) | ||
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| ## Introduction | ||
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| This Docker image includes: | ||
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| - **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 process for basecalling. | ||
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| ## Requirements | ||
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| - **Docker**: Installed on your system. | ||
| - **NVIDIA GPU and Drivers**: Installed and configured. | ||
| - **NVIDIA Container Toolkit**: To enable GPU support in Docker containers. | ||
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| ## Running the Docker Container | ||
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| To run the Dorado tool within the Docker container, use the following command: | ||
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| ```bash | ||
| docker run --gpus all -it dorado-image dorado --help | ||
| ``` | ||
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| This command will display the help information for Dorado, confirming that it's installed correctly. | ||
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| ## Testing the Docker Image | ||
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| To test that Dorado is working correctly, you will need to download a sample Pod5 file and perform a basecalling operation using the pre-downloaded basecalling models. | ||
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| ```bash | ||
| wget -O 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 | ||
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| ### Basecalling Test | ||
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| Run the following command: | ||
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| ```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" | ||
| ``` | ||
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| **Explanation:** | ||
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| - `--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. | ||
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| ### Verifying the Output | ||
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| Check the output file to ensure basecalling was successful: | ||
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| ```bash | ||
| samtools view basecalled.sam | ||
| ``` | ||
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| You should see SAM-formatted basecalling results. | ||
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| ## Additional Notes | ||
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| - **Sample Data**: The sample Pod5 file is downloaded to `/usr/src/app` during the docker image build. | ||
| - _Note: If you are using the pre-built StaPH-B docker image downloaded from dockerhub or quay.io, it will only include the `app` stage. This means that the sample Pod5 file will not be available in the container. You will need to download the sample Pod5 file manually using the `wget` example command shown above._ | ||
| - **Internal Testing**: An internal test stage is included in the Dockerfile to verify installation. | ||
| - **Basecalling Models**: All models are downloaded to `/dorado_models` during the build process. | ||
| Below is the list of basecalling models included in the Docker image: | ||
| ```yaml | ||
| modification models: | ||
| - "[email protected][email protected]" | ||
| - "[email protected][email protected]" | ||
| - "[email protected][email protected]" | ||
| - "[email protected]_5mCG_5hmCG@v0" | ||
| - "[email protected]_5mCG_5hmCG@v0" | ||
| - "[email protected]_5mCG_5hmCG@v0" | ||
| - "[email protected]_5mCG@v2" | ||
| - "[email protected]_5mCG@v2" | ||
| - "[email protected]_5mCG@v2" | ||
| - "[email protected]_5mCG@v2" | ||
| - "[email protected]_5mCG@v2" | ||
| - "[email protected]_5mCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected][email protected]" | ||
| - "[email protected]_5mC@v2" | ||
| - "[email protected]_6mA@v2" | ||
| - "[email protected]_6mA@v3" | ||
| - "[email protected]_5mC_5hmC@v1" | ||
| - "[email protected]_5mC_5hmC@v1" | ||
| - "[email protected]_5mC_5hmC@v1" | ||
| - "[email protected]_6mA@v1" | ||
| - "[email protected]_6mA@v1" | ||
| - "[email protected]_6mA@v2" | ||
| - "[email protected]_6mA@v2" | ||
| - "[email protected]_5mCG_5hmCG@v1" | ||
| - "[email protected]_5mCG_5hmCG@v1" | ||
| - "[email protected]_4mC_5mC@v1" | ||
| - "[email protected]_4mC_5mC@v1" | ||
| - "[email protected]_4mC_5mC@v2" | ||
| - "[email protected]_4mC_5mC@v2" | ||
| - "[email protected]_5mC_5hmC@v1" | ||
| - "[email protected]_5mC_5hmC@v1" | ||
| - "[email protected]_5mC_5hmC@v2" | ||
| - "[email protected]_5mC_5hmC@v2" | ||
| - "[email protected]_5mCG_5hmCG@v1" | ||
| - "[email protected]_5mCG_5hmCG@v1" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_5mCG_5hmCG@v2" | ||
| - "[email protected]_6mA@v1" | ||
| - "[email protected]_6mA@v1" | ||
| - "[email protected]_6mA@v2" | ||
| - "[email protected]_6mA@v2" | ||
| - "[email protected]_m6A_DRACH@v1" | ||
| - "[email protected]_m6A@v1" | ||
| - "[email protected]_m6A@v1" | ||
| - "[email protected]_m6A_DRACH@v1" | ||
| - "[email protected]_m6A_DRACH@v1" | ||
| - "[email protected]_pseU@v1" | ||
| - "[email protected]_pseU@v1" | ||
| - "[email protected]_m5C@v1" | ||
| - "[email protected]_m5C@v1" | ||
| - "[email protected]_inosine_m6A@v1" | ||
| - "[email protected]_inosine_m6A@v1" | ||
| - "[email protected]_m6A_DRACH@v1" | ||
| - "[email protected]_m6A_DRACH@v1" | ||
| - "[email protected]_pseU@v1" | ||
| - "[email protected]_pseU@v1" | ||
| stereo models: | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| simplex models: | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "rna002_70bps_fast@v3" | ||
| - "rna002_70bps_hac@v3" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| - "[email protected]" | ||
| ``` | ||
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| ## License | ||
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| 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. | ||
| --- |