PR changes dorado

Program_Licenses.md

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

README.md

@@ -143,6 +143,7 @@ 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></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></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> | [GitHub Repository](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/ |
@@ -369,3 +370,6 @@ Each Dockerfile lists the author(s)/maintainer(s) as a metadata `LABEL`, but the
   * [@stephenturner](https://github.com/stephenturner)
   * [@soejun](https://github.com/soejun)
   * [@taylorpaisie](https://github.com/taylorpaisie)
+  * [@fraser-combe](https://github.com/fraser-combe)
+
+

dorado/0.8.0/Dockerfile

@@ -19,9 +19,9 @@ LABEL maintainer.email="[email protected]"
 WORKDIR /usr/src/app
 
 # Install dependencies
-RUN apt-get update && apt-get install -y \
-    build-essential \
-    wget
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends wget ca-certificates && \
+    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 \
@@ -36,11 +36,6 @@ 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"]
 
@@ -49,6 +44,12 @@ CMD ["dorado"]
 # -----------------------------
 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
 

dorado/0.8.0/README.md

@@ -20,23 +20,14 @@ 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.
+- **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.
 
-## 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:
@@ -49,7 +40,12 @@ This command will display the help information for Dorado, confirming that it's
 
 ## Testing the Docker Image
 
-To test that Dorado is working correctly, perform a basecalling operation using the provided sample Pod5 file and basecalling models.
+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
 
@@ -74,16 +70,142 @@ docker run --gpus all -v $(pwd):/usr/src/app -it dorado-image bash -c "\
 Check the output file to ensure basecalling was successful:
 
 ```bash
-less basecalled.sam
+samtools view 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.
+- **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