Adds updated Dorado 0.8.3

README.md

@@ -151,7 +151,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [datasets-sars-cov-2](https://github.com/CDCgov/datasets-sars-cov-2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) | <ul><li>0.6.2</li><li>0.6.3</li><li>0.7.2</li></ul> | https://github.com/CDCgov/datasets-sars-cov-2 |
 | [diamond](https://github.com/bbuchfink/diamond) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/diamond)](https://hub.docker.com/r/staphb/diamond) | <ul><li>[2.1.9](./diamond/2.1.9)</li><li>[2.1.10](./diamond/2.1.10)</li></ul> | https://github.com/bbuchfink/diamond|
 | [dnaapler](https://hub.docker.com/r/staphb/dnaapler) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dnaapler)](https://hub.docker.com/r/staphb/dnaapler) | <ul><li>[0.1.0](dnaapler/0.1.0/)</li></ul> <ul><li>[0.4.0](dnaapler/0.4.0/)</li><li>[0.5.0](./dnaapler/0.5.0/)</li><li>[0.5.1](./dnaapler/0.5.1/)</li><li>[0.7.0](./dnaapler/0.7.0/)</li><li>[0.8.0](./dnaapler/0.8.0/)</li><li>[0.8.1](./dnaapler/0.8.1/)</li></ul> | https://github.com/gbouras13/dnaapler |
-| [dorado](https://hub.docker.com/r/staphb/dorado) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dorado)](https://hub.docker.com/r/staphb/dorado) | <ul><li>[0.8.0](dorado/0.8.0/)</li></ul> | [https://github.com/nanoporetech/dorado](https://github.com/nanoporetech/dorado) |
+| [dorado](https://hub.docker.com/r/staphb/dorado) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dorado)](https://hub.docker.com/r/staphb/dorado) | <ul><li>[0.8.0](dorado/0.8.0/)</li><li>[0.8.3](dorado/0.8.3/)</li></ul> | [https://github.com/nanoporetech/dorado](https://github.com/nanoporetech/dorado) |
 | [dragonflye](https://hub.docker.com/r/staphb/dragonflye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | <ul><li>[1.0.14](./dragonflye/1.0.14/)</li><li>[1.1.1](./dragonflye/1.1.1/)</li><li>[1.1.2](./dragonflye/1.1.2/)</li><li>[1.2.0](./dragonflye/1.2.0/)</li><li>[1.2.1](./dragonflye/1.2.1/)</li></ul> | https://github.com/rpetit3/dragonflye |
 | [Dr. PRG ](https://hub.docker.com/r/staphb/drprg) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/drprg)](https://hub.docker.com/r/staphb/drprg) | <ul><li>[0.1.1](drprg/0.1.1/)</li></ul> | https://mbh.sh/drprg/ |
 | [DSK](https://hub.docker.com/r/staphb/dsk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | <ul><li>[0.0.100](./dsk/0.0.100/)</li><li>[2.3.3](./dsk/2.3.3/)</li></ul> | https://gatb.inria.fr/software/dsk/ |

dorado/0.8.3/Dockerfile

@@ -0,0 +1,64 @@
+# Use NVIDIA CUDA image as the base image
+FROM nvidia/cuda:12.2.0-devel-ubuntu20.04 AS app
+
+ARG DORADO_VER=0.8.3
+
+# 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 --no-install-recommends wget ca-certificates pigz && \
+    rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+# 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
+
+# Default command
+CMD ["dorado"]
+
+# -----------------------------
+# Test Stage
+# -----------------------------
+FROM app AS test
+
+
+# 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
+
+# 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/0.8.3/README.md

@@ -0,0 +1,220 @@
+# 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 **0.8.3**, a tool for basecalling Oxford Nanopore sequencing data.
+- **NVIDIA CUDA**: Version **12.2.0**, for GPU acceleration (requires NVIDIA GPU).
+- **Pigz**: Version **2.6**, for parallel compression and decompression.
+- **Pre-downloaded basecalling models**: All models are downloaded during the build process for basecalling.
+
+## Requirements
+
+- **Docker**: Installed on your system.
+- **NVIDIA GPU and Drivers**: Installed and configured.
+- **NVIDIA Container Toolkit**: To enable GPU support in Docker containers.
+
+## 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, you will need to download a sample Pod5 file and perform a basecalling operation using the pre-downloaded basecalling models.
+
+```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
+
+
+### 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
+samtools view basecalled.sam
+```
+
+You should see SAM-formatted basecalling results.
+
+## Additional Notes
+
+- **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.
+- **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]"
+  ```
+
+## 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.
+
+---