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‎Program_Licenses.md‎

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@@ -38,6 +38,7 @@ The licenses of the open-source software that is contained in these Docker image
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| datasets-sars-cov-2 | Apache 2.0 | https://github.com/CDCgov/datasets-sars-cov-2/blob/master/LICENSE |
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| diamond | GNU GPLv3 | https://github.com/bbuchfink/diamond/blob/master/LICENSE |
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| dnaapler | MIT | https://github.com/gbouras13/dnaapler/blob/main/LICENSE |
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| dorado | Oxford Nanopore Technologies PLC Public License | [ONT License](https://github.com/nanoporetech/dorado/blob/master/LICENSE) |
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| dragonflye | GNU GPLv3 | https://github.com/rpetit3/dragonflye/blob/main/LICENSE |
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| drprg | MIT | https://github.com/mbhall88/drprg/blob/main/LICENSE |
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| DSK | GNU Affero GPLv3 | https://github.com/GATB/dsk/blob/master/LICENSE |

‎README.md‎

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@@ -143,6 +143,7 @@ To learn more about the docker pull rate limits and the open source software pro
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| [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 |
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| [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></ul> | https://github.com/bbuchfink/diamond|
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| [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></ul> | https://github.com/gbouras13/dnaapler |
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| [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> | [GitHub Repository](https://github.com/nanoporetech/dorado) |
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| [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 |
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| [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/ |
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| [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/ |
@@ -369,3 +370,6 @@ Each Dockerfile lists the author(s)/maintainer(s) as a metadata `LABEL`, but the
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* [@stephenturner](https://github.com/stephenturner)
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* [@soejun](https://github.com/soejun)
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* [@taylorpaisie](https://github.com/taylorpaisie)
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* [@fraser-combe](https://github.com/fraser-combe)
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‎dorado/0.8.0/Dockerfile‎

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@@ -19,9 +19,9 @@ LABEL maintainer.email="fraser.combe@theiagen.com"
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WORKDIR /usr/src/app
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# Install dependencies
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RUN apt-get update && apt-get install -y \
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build-essential \
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wget
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RUN apt-get update && \
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apt-get install -y --no-install-recommends wget ca-certificates && \
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rm -rf /var/lib/apt/lists/* && apt-get autoclean
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# Download and extract Dorado package
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RUN wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-${DORADO_VER}-linux-x64.tar.gz \
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cd /dorado_models && \
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dorado download --model all
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# Download the specific Pod5 test file
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RUN wget -O /usr/src/app/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 \
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https://github.com/nanoporetech/dorado/raw/release-v0.7/tests/data/pod5/dna_r10.4.1_e8.2_260bps/\
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dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5
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# Default command
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CMD ["dorado"]
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# -----------------------------
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FROM app AS test
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# Download the specific Pod5 test file
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RUN wget -O /usr/src/app/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 \
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https://github.com/nanoporetech/dorado/raw/release-v0.7/tests/data/pod5/dna_r10.4.1_e8.2_260bps/\
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dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5
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# Set working directory
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WORKDIR /usr/src/app
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‎dorado/0.8.0/README.md‎

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- **Dorado**: Version **0.8.0**, a tool for basecalling Oxford Nanopore sequencing data.
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- **NVIDIA CUDA**: Version **12.2.0**, for GPU acceleration (requires NVIDIA GPU).
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- **Pre-downloaded basecalling models**: All models are downloaded during the build.
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- **Sample Pod5 test file**: Included for testing the basecalling process.
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- **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.
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- **NVIDIA GPU and Drivers**: Installed and configured.
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- **NVIDIA Container Toolkit**: To enable GPU support in Docker containers.
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## Building the Docker Image
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**Build the Docker image** using the following command:
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```bash
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docker build -t dorado-image .
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```
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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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## Testing the Docker Image
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To test that Dorado is working correctly, perform a basecalling operation using the provided sample Pod5 file and basecalling models.
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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
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wget -O dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 \
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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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Check the output file to ensure basecalling was successful:
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```bash
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less basecalled.sam
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samtools view basecalled.sam
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```
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You should see SAM-formatted basecalling results.
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## Additional Notes
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- **Basecalling Models**: All models are downloaded to `/dorado_models` during the build process.
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- **Sample Data**: The sample Pod5 file is downloaded to `/usr/src/app` during the build.
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- **Internal Testing**: An internal test stage is included in the Dockerfile to verify installation.
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- **Basecalling Models**: All models are downloaded to `/dorado_models` during the build process.
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Below is the list of basecalling models included in the Docker image:
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```yaml
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modification models:
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- "dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1"
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- "dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1"
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- "dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1"
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- "dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0"
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- "dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0"
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- "dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0"
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- "dna_r10.4.1_e8.2_260bps_fast@v3.5.2_5mCG@v2"
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- "dna_r10.4.1_e8.2_260bps_hac@v3.5.2_5mCG@v2"
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- "dna_r10.4.1_e8.2_260bps_sup@v3.5.2_5mCG@v2"
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- "dna_r10.4.1_e8.2_400bps_fast@v3.5.2_5mCG@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v3.5.2_5mCG@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v3.5.2_5mCG@v2"
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- "dna_r10.4.1_e8.2_260bps_fast@v4.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_260bps_hac@v4.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_260bps_sup@v4.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_fast@v4.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.2.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v3.1"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v3"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC_5hmC@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v1"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v2"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v2"
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- "rna004_130bps_sup@v3.0.1_m6A_DRACH@v1"
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- "rna004_130bps_hac@v5.0.0_m6A@v1"
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- "rna004_130bps_sup@v5.0.0_m6A@v1"
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- "rna004_130bps_hac@v5.0.0_m6A_DRACH@v1"
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- "rna004_130bps_sup@v5.0.0_m6A_DRACH@v1"
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- "rna004_130bps_hac@v5.0.0_pseU@v1"
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- "rna004_130bps_sup@v5.0.0_pseU@v1"
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- "rna004_130bps_hac@v5.1.0_m5C@v1"
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- "rna004_130bps_sup@v5.1.0_m5C@v1"
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- "rna004_130bps_hac@v5.1.0_inosine_m6A@v1"
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- "rna004_130bps_sup@v5.1.0_inosine_m6A@v1"
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- "rna004_130bps_hac@v5.1.0_m6A_DRACH@v1"
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- "rna004_130bps_sup@v5.1.0_m6A_DRACH@v1"
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- "rna004_130bps_hac@v5.1.0_pseU@v1"
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- "rna004_130bps_sup@v5.1.0_pseU@v1"
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stereo models:
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- "dna_r10.4.1_e8.2_4khz_stereo@v1.1"
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- "dna_r10.4.1_e8.2_4khz_stereo@v1.1"
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- "dna_r10.4.1_e8.2_5khz_stereo@v1.1"
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- "dna_r10.4.1_e8.2_5khz_stereo@v1.2"
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- "dna_r10.4.1_e8.2_5khz_stereo@v1.3"
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simplex models:
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- "dna_r9.4.1_e8_fast@v3.4"
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- "dna_r9.4.1_e8_hac@v3.3"
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- "dna_r9.4.1_e8_sup@v3.3"
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- "dna_r9.4.1_e8_sup@v3.6"
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- "dna_r10.4.1_e8.2_260bps_fast@v3.5.2"
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- "dna_r10.4.1_e8.2_260bps_hac@v3.5.2"
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- "dna_r10.4.1_e8.2_260bps_sup@v3.5.2"
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- "dna_r10.4.1_e8.2_400bps_fast@v3.5.2"
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- "dna_r10.4.1_e8.2_400bps_hac@v3.5.2"
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- "dna_r10.4.1_e8.2_400bps_sup@v3.5.2"
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- "dna_r10.4.1_e8.2_260bps_fast@v4.0.0"
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- "dna_r10.4.1_e8.2_260bps_hac@v4.0.0"
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- "dna_r10.4.1_e8.2_260bps_sup@v4.0.0"
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- "dna_r10.4.1_e8.2_400bps_fast@v4.0.0"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.0.0"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.0.0"
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- "dna_r10.4.1_e8.2_260bps_fast@v4.1.0"
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- "dna_r10.4.1_e8.2_260bps_hac@v4.1.0"
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- "dna_r10.4.1_e8.2_260bps_sup@v4.1.0"
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- "dna_r10.4.1_e8.2_400bps_fast@v4.1.0"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.1.0"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.1.0"
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- "dna_r10.4.1_e8.2_400bps_fast@v4.2.0"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.2.0"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.2.0"
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- "dna_r10.4.1_e8.2_400bps_fast@v4.3.0"
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- "dna_r10.4.1_e8.2_400bps_hac@v4.3.0"
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- "dna_r10.4.1_e8.2_400bps_sup@v4.3.0"
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- "dna_r10.4.1_e8.2_400bps_fast@v5.0.0"
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- "dna_r10.4.1_e8.2_400bps_hac@v5.0.0"
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- "dna_r10.4.1_e8.2_400bps_sup@v5.0.0"
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- "dna_r10.4.1_e8.2_apk_sup@v5.0.0"
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- "rna002_70bps_fast@v3"
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- "rna002_70bps_hac@v3"
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- "rna004_130bps_fast@v3.0.1"
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- "rna004_130bps_hac@v3.0.1"
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- "rna004_130bps_sup@v3.0.1"
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- "rna004_130bps_fast@v5.0.0"
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- "rna004_130bps_hac@v5.0.0"
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- "rna004_130bps_sup@v5.0.0"
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- "rna004_130bps_fast@v5.1.0"
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- "rna004_130bps_hac@v5.1.0"
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- "rna004_130bps_sup@v5.1.0"
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```
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## License
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