adds dorado 0.8.3 no-model

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) <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><li>[2.1.10](./diamond/2.1.10)</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><li>[0.8.1](./dnaapler/0.8.1/)</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><li>[0.8.3](dorado/0.8.3/)</li></ul> | [https://github.com/nanoporetech/dorado](https://github.com/nanoporetech/dorado) |
+| [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><li>[0.8.3](dorado/0.8.3/)</li><li>[0.8.3-cuda12.4.0-no_model](./dorado/0.8.3/)</li></ul> | [https://github.com/nanoporetech/dorado](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/ |

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
+

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.</br>
+Cuda dirivers >= 12.4.0 are required for gpu support.</br>
+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
+```
+