This Dockerfile sets up an environment for running Dorado, a tool for basecalling Fast5/Pod5 files from Oxford Nanopore sequencing.
- Introduction
- Requirements
- Running the Docker Container
- Testing the Docker Image
- Basecalling Test
- Verifying the Output
- Additional Notes
This Docker image includes:
- Dorado: Version 0.9.0, 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. They are located at
/dorado_models/in the container filesystem.
- Docker: Installed on your system.
- NVIDIA GPU and Drivers: Installed and configured.
- NVIDIA Container Toolkit: To enable GPU support in Docker containers.
To run the Dorado tool within the Docker container, use the following command:
docker run --gpus all -it staphb/dorado:latest dorado --helpThis command will display the help information for Dorado, confirming that it's installed correctly.
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.
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# Run the following command:
docker run --gpus all -v $(pwd):/usr/src/app -it staphb/dorado:latest 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/appinside the container.bash -c "...":Runs the basecalling command inside the container.> /usr/src/app/basecalled.sam: Redirects the output tobasecalled.samin your current directory.
Check the output file to ensure basecalling was successful:
samtools view basecalled.samYou should see SAM-formatted basecalling results.
- Sample Data: The sample Pod5 file is downloaded to
/usr/src/appduring the build. - Internal Testing: An internal test stage is included in the Dockerfile to verify installation.
- Basecalling Models: All models are downloaded to
/dorado_modelsduring the build process. Below is the list of basecalling models included in the Docker image:
# modification models:
- [email protected]
- [email protected]_5mCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]
- [email protected]
- [email protected]_5mCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v1
- [email protected]_5mC_5hmC@v1
- [email protected]_6mA@v1
- [email protected]_6mA@v2
- [email protected]
- [email protected]_4mC_5mC@v1
- [email protected]_4mC_5mC@v2
- [email protected]_4mC_5mC@v3
- [email protected]_5mCG_5hmCG@v1
- [email protected]_5mCG_5hmCG@v2
- [email protected]_5mCG_5hmCG@v3
- [email protected]_5mC_5hmC@v1
- [email protected]_5mC_5hmC@v2
- [email protected]_5mC_5hmC@v3
- [email protected]_6mA@v1
- [email protected]_6mA@v2
- [email protected]_6mA@v3
- [email protected]
- [email protected]_5mCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mCG_5hmCG@v2
- [email protected]
- [email protected]_5mC@v2
- [email protected]_5mCG_5hmCG@v2
- [email protected][email protected]
- [email protected]_5mC_5hmC@v1
- [email protected]_6mA@v2
- [email protected]_6mA@v3
- [email protected]
- [email protected]_5mCG_5hmCG@v1
- [email protected]_5mC_5hmC@v1
- [email protected]_6mA@v1
- [email protected]_6mA@v2
- [email protected]
- [email protected]_4mC_5mC@v1
- [email protected]_4mC_5mC@v2
- [email protected]_4mC_5mC@v3
- [email protected]_5mCG_5hmCG@v1
- [email protected][email protected]
- [email protected]_5mCG_5hmCG@v3
- [email protected]_5mC_5hmC@v1
- [email protected][email protected]
- [email protected]_5mC_5hmC@v3
- [email protected]_6mA@v1
- [email protected]_6mA@v2
- [email protected]_6mA@v3
- [email protected]
- [email protected]
- [email protected]
- [email protected]
- [email protected]
- [email protected]
- [email protected][email protected]
- [email protected]_5mCG_5hmCG@v0
- [email protected]
- [email protected][email protected]
- [email protected]_5mCG_5hmCG@v0
- [email protected]
- [email protected][email protected]
- [email protected]_5mCG_5hmCG@v0
- [email protected]
- rna002_70bps_fast@v3
- rna002_70bps_hac@v3
- [email protected]
- [email protected]
- [email protected]
- [email protected]
- [email protected]
- [email protected]_m6A@v1
- [email protected]_m6A_DRACH@v1
- [email protected]_pseU@v1
- [email protected]
- [email protected]_inosine_m6A@v1
- [email protected]_m5C@v1
- [email protected]_m6A_DRACH@v1
- [email protected]_pseU@v1
- [email protected]
- [email protected]_m6A_DRACH@v1
- [email protected]
- [email protected]_m6A@v1
- [email protected]_m6A_DRACH@v1
- [email protected]_pseU@v1
- [email protected]
- [email protected]_inosine_m6A@v1
- [email protected]_m5C@v1
- [email protected]_m6A_DRACH@v1
- [email protected]_pseU@v1Note: Please ensure that you have the necessary NVIDIA drivers and the NVIDIA Container Toolkit installed to utilize GPU acceleration.