diff --git a/README.md b/README.md index 686accabf..300be6e78 100644 --- a/README.md +++ b/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)
[![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) | | [https://github.com/nanoporetech/dorado](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) | | [https://github.com/nanoporetech/dorado](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/ | diff --git a/dorado/0.8.3-cuda12.4.0-no_model/Dockerfile b/dorado/0.8.3-cuda12.4.0-no_model/Dockerfile new file mode 100644 index 000000000..e85ec1e8f --- /dev/null +++ b/dorado/0.8.3-cuda12.4.0-no_model/Dockerfile @@ -0,0 +1,39 @@ +FROM nvidia/cuda:12.4.0-base-ubuntu22.04 AS app + +ARG DORADO_VER="0.8.3" + +LABEL base.image="nvidia/cuda:12.4.0-base-ubuntu20.04" +LABEL dockerfile.version="1" +LABEL software="Dorado" +LABEL software.version="${DORADO_VER}" +LABEL description="A tool for basecalling Fast5/Pod5 files from Oxford Nanopore sequencing" +LABEL website="https://github.com/nanoporetech/dorado" +LABEL license="https://github.com/nanoporetech/dorado/blob/master/LICENSE" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y\ + wget \ + pigz \ + procps &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget -q --no-check-certificate https://cdn.oxfordnanoportal.com/software/analysis/dorado-${DORADO_VER}-linux-x64.tar.gz &&\ + tar --strip-components=1 -C /usr/local/ -xvf dorado-${DORADO_VER}-linux-x64.tar.gz &&\ + rm dorado-${DORADO_VER}-linux-x64.tar.gz + +ENV LC_ALL=C + +CMD ["dorado", "-h"] + +WORKDIR /data + +## Test ## +FROM app AS test + +ADD https://github.com/nanoporetech/dorado/raw/release-v0.8/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 dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 + +RUN dorado download --model dna_r10.4.1_e8.2_260bps_sup@v3.5.2 &&\ + dorado basecaller 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 > calls.bam &&\ + dorado summary calls.bam + diff --git a/dorado/0.8.3-cuda12.4.0-no_model/README.md b/dorado/0.8.3-cuda12.4.0-no_model/README.md new file mode 100644 index 000000000..73c279469 --- /dev/null +++ b/dorado/0.8.3-cuda12.4.0-no_model/README.md @@ -0,0 +1,33 @@ +# Dorada container + +Main tool: [dorado](https://github.com/nanoporetech/dorado) + +Code repository: https://github.com/nanoporetech/dorado + +Basic information on how to use this tool: +- executable: dorado +- help: -h, --help +- version: -v, --version +- description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. + +Additional information: + +This container does not contain any models.
+Cuda dirivers >= 12.4.0 are required for gpu support.
+Use **"--gpus all"** flag to activate gpu support in docker. E.g. +`docker run -it --gpus all staphb/dorado:0.8.3-cuda12.4.0-no_model bash` + +Full documentation: https://dorado-docs.readthedocs.io/en/latest/ + +## Example Usage +```bash +# list models +dorado download --list +# downlaod a single model +dorado download --model {model_name} +# download all models +dorado download +# basecaller +dorado basecaller {model} {data} > calls.bam +``` +