From bc499b0db18a5ba0dbff8c5269adc652d44c05f8 Mon Sep 17 00:00:00 2001 From: Fraser Combe Date: Fri, 20 Sep 2024 18:35:38 +0000 Subject: [PATCH 1/5] Add Dorado 0.8.0 Dockerfile and README --- dorado/0.8.0/Dockerfile | 63 ++++++++++++++++++++++++++ dorado/0.8.0/README.md | 97 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 160 insertions(+) create mode 100755 dorado/0.8.0/Dockerfile create mode 100644 dorado/0.8.0/README.md diff --git a/dorado/0.8.0/Dockerfile b/dorado/0.8.0/Dockerfile new file mode 100755 index 000000000..d5664657d --- /dev/null +++ b/dorado/0.8.0/Dockerfile @@ -0,0 +1,63 @@ +# Use NVIDIA CUDA image as the base image +FROM nvidia/cuda:12.2.0-devel-ubuntu20.04 AS app + +ARG DORADO_VER=0.8.0 + +# 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="fraser.combe@theiagen.com" + +# Set working directory +WORKDIR /usr/src/app + +# Install dependencies +RUN apt-get update && apt-get install -y \ + build-essential \ + wget + +# 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 + +# 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"] + +# ----------------------------- +# Test Stage +# ----------------------------- +FROM app AS test + +# Set working directory +WORKDIR /usr/src/app + +# Run test command (using CPU mode) +RUN dorado basecaller \ + --device cpu \ + /dorado_models/dna_r10.4.1_e8.2_260bps_sup@v3.5.2 \ + 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 diff --git a/dorado/0.8.0/README.md b/dorado/0.8.0/README.md new file mode 100644 index 000000000..0fbc039ff --- /dev/null +++ b/dorado/0.8.0/README.md @@ -0,0 +1,97 @@ +# 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 **0.8.0**, 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. + +## 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: + +```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, perform a basecalling operation using the provided sample Pod5 file and basecalling models. + +### 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/dna_r10.4.1_e8.2_260bps_sup@v3.5.2 \ + /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 +less 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. + +## 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. + +--- From 4ca165b215dbb23f440869dfa9e82939bcea9fb4 Mon Sep 17 00:00:00 2001 From: Fraser Combe Date: Mon, 23 Sep 2024 15:03:41 +0000 Subject: [PATCH 2/5] PR changes dorado --- Program_Licenses.md | 1 + README.md | 4 ++ dorado/0.8.0/Dockerfile | 17 ++--- dorado/0.8.0/README.md | 148 ++++++++++++++++++++++++++++++++++++---- 4 files changed, 149 insertions(+), 21 deletions(-) diff --git a/Program_Licenses.md b/Program_Licenses.md index 1479c2fd6..608b3b95e 100644 --- a/Program_Licenses.md +++ b/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 | diff --git a/README.md b/README.md index 21009f913..0c09f1445 100644 --- a/README.md +++ b/README.md @@ -148,6 +148,7 @@ 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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) | | https://github.com/CDCgov/datasets-sars-cov-2 | | [diamond](https://github.com/bbuchfink/diamond)
[![docker pulls](https://badgen.net/docker/pulls/staphb/diamond)](https://hub.docker.com/r/staphb/diamond) | | https://github.com/bbuchfink/diamond| | [dnaapler](https://hub.docker.com/r/staphb/dnaapler)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dnaapler)](https://hub.docker.com/r/staphb/dnaapler) | | https://github.com/gbouras13/dnaapler | +| [dorado](https://hub.docker.com/r/staphb/dorado)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dorado)](https://hub.docker.com/r/staphb/dorado) | | [GitHub Repository](https://github.com/nanoporetech/dorado) | | [dragonflye](https://hub.docker.com/r/staphb/dragonflye)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | | https://github.com/rpetit3/dragonflye | | [Dr. PRG ](https://hub.docker.com/r/staphb/drprg)
[![docker pulls](https://badgen.net/docker/pulls/staphb/drprg)](https://hub.docker.com/r/staphb/drprg) | | https://mbh.sh/drprg/ | | [DSK](https://hub.docker.com/r/staphb/dsk)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | | https://gatb.inria.fr/software/dsk/ | @@ -375,3 +376,6 @@ 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) + + diff --git a/dorado/0.8.0/Dockerfile b/dorado/0.8.0/Dockerfile index d5664657d..523efa26f 100755 --- a/dorado/0.8.0/Dockerfile +++ b/dorado/0.8.0/Dockerfile @@ -19,9 +19,9 @@ LABEL maintainer.email="fraser.combe@theiagen.com" 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 diff --git a/dorado/0.8.0/README.md b/dorado/0.8.0/README.md index 0fbc039ff..82534b3a3 100644 --- a/dorado/0.8.0/README.md +++ b/dorado/0.8.0/README.md @@ -20,8 +20,7 @@ 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 @@ -29,14 +28,6 @@ This Docker image includes: - **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: + - "dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1" + - "dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1" + - "dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1" + - "dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0" + - "dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0" + - "dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0" + - "dna_r10.4.1_e8.2_260bps_fast@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_260bps_hac@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_260bps_sup@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_260bps_fast@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_hac@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_sup@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.2.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v3.1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v3" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v2" + - "rna004_130bps_sup@v3.0.1_m6A_DRACH@v1" + - "rna004_130bps_hac@v5.0.0_m6A@v1" + - "rna004_130bps_sup@v5.0.0_m6A@v1" + - "rna004_130bps_hac@v5.0.0_m6A_DRACH@v1" + - "rna004_130bps_sup@v5.0.0_m6A_DRACH@v1" + - "rna004_130bps_hac@v5.0.0_pseU@v1" + - "rna004_130bps_sup@v5.0.0_pseU@v1" + - "rna004_130bps_hac@v5.1.0_m5C@v1" + - "rna004_130bps_sup@v5.1.0_m5C@v1" + - "rna004_130bps_hac@v5.1.0_inosine_m6A@v1" + - "rna004_130bps_sup@v5.1.0_inosine_m6A@v1" + - "rna004_130bps_hac@v5.1.0_m6A_DRACH@v1" + - "rna004_130bps_sup@v5.1.0_m6A_DRACH@v1" + - "rna004_130bps_hac@v5.1.0_pseU@v1" + - "rna004_130bps_sup@v5.1.0_pseU@v1" + stereo models: + - "dna_r10.4.1_e8.2_4khz_stereo@v1.1" + - "dna_r10.4.1_e8.2_4khz_stereo@v1.1" + - "dna_r10.4.1_e8.2_5khz_stereo@v1.1" + - "dna_r10.4.1_e8.2_5khz_stereo@v1.2" + - "dna_r10.4.1_e8.2_5khz_stereo@v1.3" + simplex models: + - "dna_r9.4.1_e8_fast@v3.4" + - "dna_r9.4.1_e8_hac@v3.3" + - "dna_r9.4.1_e8_sup@v3.3" + - "dna_r9.4.1_e8_sup@v3.6" + - "dna_r10.4.1_e8.2_260bps_fast@v3.5.2" + - "dna_r10.4.1_e8.2_260bps_hac@v3.5.2" + - "dna_r10.4.1_e8.2_260bps_sup@v3.5.2" + - "dna_r10.4.1_e8.2_400bps_fast@v3.5.2" + - "dna_r10.4.1_e8.2_400bps_hac@v3.5.2" + - "dna_r10.4.1_e8.2_400bps_sup@v3.5.2" + - "dna_r10.4.1_e8.2_260bps_fast@v4.0.0" + - "dna_r10.4.1_e8.2_260bps_hac@v4.0.0" + - "dna_r10.4.1_e8.2_260bps_sup@v4.0.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.0.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.0.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.0.0" + - "dna_r10.4.1_e8.2_260bps_fast@v4.1.0" + - "dna_r10.4.1_e8.2_260bps_hac@v4.1.0" + - "dna_r10.4.1_e8.2_260bps_sup@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.2.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.2.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.3.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0" + - "dna_r10.4.1_e8.2_400bps_fast@v5.0.0" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0" + - "dna_r10.4.1_e8.2_apk_sup@v5.0.0" + - "rna002_70bps_fast@v3" + - "rna002_70bps_hac@v3" + - "rna004_130bps_fast@v3.0.1" + - "rna004_130bps_hac@v3.0.1" + - "rna004_130bps_sup@v3.0.1" + - "rna004_130bps_fast@v5.0.0" + - "rna004_130bps_hac@v5.0.0" + - "rna004_130bps_sup@v5.0.0" + - "rna004_130bps_fast@v5.1.0" + - "rna004_130bps_hac@v5.1.0" + - "rna004_130bps_sup@v5.1.0" + ``` ## License From f7759b7f29e647ae4f234235c5b5087ce0c0813e Mon Sep 17 00:00:00 2001 From: Fraser Combe Date: Tue, 19 Nov 2024 22:20:53 +0000 Subject: [PATCH 3/5] Dorado version 0.8.3 --- README.md | 2 +- dorado/0.8.3/Dockerfile | 64 ++++++++++++ dorado/0.8.3/README.md | 220 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 285 insertions(+), 1 deletion(-) create mode 100644 dorado/0.8.3/Dockerfile create mode 100644 dorado/0.8.3/README.md diff --git a/README.md b/README.md index 0c09f1445..2b9614f86 100644 --- a/README.md +++ b/README.md @@ -148,7 +148,7 @@ 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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) |
  • 0.6.2
  • 0.6.3
  • 0.7.2
| https://github.com/CDCgov/datasets-sars-cov-2 | | [diamond](https://github.com/bbuchfink/diamond)
[![docker pulls](https://badgen.net/docker/pulls/staphb/diamond)](https://hub.docker.com/r/staphb/diamond) |
  • [2.1.9](./diamond/2.1.9)
| https://github.com/bbuchfink/diamond| | [dnaapler](https://hub.docker.com/r/staphb/dnaapler)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dnaapler)](https://hub.docker.com/r/staphb/dnaapler) |
  • [0.1.0](dnaapler/0.1.0/)
  • [0.4.0](dnaapler/0.4.0/)
  • [0.5.0](dnaapler/0.5.0/)
  • [0.5.1](dnaapler/0.5.1/)
  • [0.7.0](dnaapler/0.7.0/)
  • [0.8.0](dnaapler/0.8.0/)
| https://github.com/gbouras13/dnaapler | -| [dorado](https://hub.docker.com/r/staphb/dorado)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dorado)](https://hub.docker.com/r/staphb/dorado) |
  • [0.8.0](dorado/0.8.0/)
| [GitHub Repository](https://github.com/nanoporetech/dorado) | +| [dorado](https://hub.docker.com/r/staphb/dorado)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dorado)](https://hub.docker.com/r/staphb/dorado) |
  • [0.8.3](dorado/0.8.0/)
| [GitHub Repository](https://github.com/nanoporetech/dorado) | | [dragonflye](https://hub.docker.com/r/staphb/dragonflye)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) |
  • [1.0.14](./dragonflye/1.0.14/)
  • [1.1.1](./dragonflye/1.1.1/)
  • [1.1.2](./dragonflye/1.1.2/)
  • [1.2.0](./dragonflye/1.2.0/)
  • [1.2.1](./dragonflye/1.2.1/)
| https://github.com/rpetit3/dragonflye | | [Dr. PRG ](https://hub.docker.com/r/staphb/drprg)
[![docker pulls](https://badgen.net/docker/pulls/staphb/drprg)](https://hub.docker.com/r/staphb/drprg) |
  • [0.1.1](drprg/0.1.1/)
| https://mbh.sh/drprg/ | | [DSK](https://hub.docker.com/r/staphb/dsk)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) |
  • [0.0.100](./dsk/0.0.100/)
  • [2.3.3](./dsk/2.3.3/)
| https://gatb.inria.fr/software/dsk/ | diff --git a/dorado/0.8.3/Dockerfile b/dorado/0.8.3/Dockerfile new file mode 100644 index 000000000..bd9116b74 --- /dev/null +++ b/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="fraser.combe@theiagen.com" + +# 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/dna_r10.4.1_e8.2_260bps_sup@v3.5.2 \ + 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 diff --git a/dorado/0.8.3/README.md b/dorado/0.8.3/README.md new file mode 100644 index 000000000..54cd743c1 --- /dev/null +++ b/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/dna_r10.4.1_e8.2_260bps_sup@v3.5.2 \ + /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: + - "dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1" + - "dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1" + - "dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1" + - "dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0" + - "dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0" + - "dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0" + - "dna_r10.4.1_e8.2_260bps_fast@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_260bps_hac@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_260bps_sup@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v3.5.2_5mCG@v2" + - "dna_r10.4.1_e8.2_260bps_fast@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_hac@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_sup@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.2.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v3.1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v3" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v2" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v2" + - "rna004_130bps_sup@v3.0.1_m6A_DRACH@v1" + - "rna004_130bps_hac@v5.0.0_m6A@v1" + - "rna004_130bps_sup@v5.0.0_m6A@v1" + - "rna004_130bps_hac@v5.0.0_m6A_DRACH@v1" + - "rna004_130bps_sup@v5.0.0_m6A_DRACH@v1" + - "rna004_130bps_hac@v5.0.0_pseU@v1" + - "rna004_130bps_sup@v5.0.0_pseU@v1" + - "rna004_130bps_hac@v5.1.0_m5C@v1" + - "rna004_130bps_sup@v5.1.0_m5C@v1" + - "rna004_130bps_hac@v5.1.0_inosine_m6A@v1" + - "rna004_130bps_sup@v5.1.0_inosine_m6A@v1" + - "rna004_130bps_hac@v5.1.0_m6A_DRACH@v1" + - "rna004_130bps_sup@v5.1.0_m6A_DRACH@v1" + - "rna004_130bps_hac@v5.1.0_pseU@v1" + - "rna004_130bps_sup@v5.1.0_pseU@v1" + stereo models: + - "dna_r10.4.1_e8.2_4khz_stereo@v1.1" + - "dna_r10.4.1_e8.2_4khz_stereo@v1.1" + - "dna_r10.4.1_e8.2_5khz_stereo@v1.1" + - "dna_r10.4.1_e8.2_5khz_stereo@v1.2" + - "dna_r10.4.1_e8.2_5khz_stereo@v1.3" + simplex models: + - "dna_r9.4.1_e8_fast@v3.4" + - "dna_r9.4.1_e8_hac@v3.3" + - "dna_r9.4.1_e8_sup@v3.3" + - "dna_r9.4.1_e8_sup@v3.6" + - "dna_r10.4.1_e8.2_260bps_fast@v3.5.2" + - "dna_r10.4.1_e8.2_260bps_hac@v3.5.2" + - "dna_r10.4.1_e8.2_260bps_sup@v3.5.2" + - "dna_r10.4.1_e8.2_400bps_fast@v3.5.2" + - "dna_r10.4.1_e8.2_400bps_hac@v3.5.2" + - "dna_r10.4.1_e8.2_400bps_sup@v3.5.2" + - "dna_r10.4.1_e8.2_260bps_fast@v4.0.0" + - "dna_r10.4.1_e8.2_260bps_hac@v4.0.0" + - "dna_r10.4.1_e8.2_260bps_sup@v4.0.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.0.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.0.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.0.0" + - "dna_r10.4.1_e8.2_260bps_fast@v4.1.0" + - "dna_r10.4.1_e8.2_260bps_hac@v4.1.0" + - "dna_r10.4.1_e8.2_260bps_sup@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.1.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.2.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.2.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0" + - "dna_r10.4.1_e8.2_400bps_fast@v4.3.0" + - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0" + - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0" + - "dna_r10.4.1_e8.2_400bps_fast@v5.0.0" + - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0" + - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0" + - "dna_r10.4.1_e8.2_apk_sup@v5.0.0" + - "rna002_70bps_fast@v3" + - "rna002_70bps_hac@v3" + - "rna004_130bps_fast@v3.0.1" + - "rna004_130bps_hac@v3.0.1" + - "rna004_130bps_sup@v3.0.1" + - "rna004_130bps_fast@v5.0.0" + - "rna004_130bps_hac@v5.0.0" + - "rna004_130bps_sup@v5.0.0" + - "rna004_130bps_fast@v5.1.0" + - "rna004_130bps_hac@v5.1.0" + - "rna004_130bps_sup@v5.1.0" + ``` + +## 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. + +--- From ee378cd741899468d742456a3af664b076bd4df0 Mon Sep 17 00:00:00 2001 From: Fraser Combe Date: Wed, 20 Nov 2024 17:14:32 +0000 Subject: [PATCH 4/5] update 0.8.0 files --- Program_Licenses.md | 2 +- dorado/0.8.0/README.md | 6 ------ 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/Program_Licenses.md b/Program_Licenses.md index 11332ca10..22d258921 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -41,7 +41,7 @@ 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) | +| dorado | Oxford Nanopore Technologies PLC Public License | [ONT License](https://github.com/nanoporetech/dorado/blob/master/LICENSE.txt) | | 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 | diff --git a/dorado/0.8.0/README.md b/dorado/0.8.0/README.md index 42a82a02b..9267d7ce5 100644 --- a/dorado/0.8.0/README.md +++ b/dorado/0.8.0/README.md @@ -46,10 +46,6 @@ To test that Dorado is working correctly, you will need to download a sample Pod 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: @@ -80,8 +76,6 @@ You should see SAM-formatted basecalling results. ## Additional Notes - -- **Sample Data**: The sample Pod5 file is downloaded to `/usr/src/app` during the build. - **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. From e81eb8fa219ce10dd804555fbb9e20795e9bd773 Mon Sep 17 00:00:00 2001 From: Fraser Combe Date: Wed, 20 Nov 2024 17:15:31 +0000 Subject: [PATCH 5/5] correct licence --- Program_Licenses.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Program_Licenses.md b/Program_Licenses.md index 22d258921..7e0049c8e 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -41,7 +41,7 @@ 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.txt) | +| dorado | Oxford Nanopore Technologies PLC Public License | [ONT License](https://github.com/nanoporetech/dorado/blob/master/LICENCE.txt) | | 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 |