Update Dorado to 1.4.0 version (#1562)

* Create README.md for 1.4.0

* Create Dockerfile fop dorado cuda 13

* Update Dockerfile

* Rename dorado folder to 1.4.0-cuda13.1.1

* Update README.md with new cuba version

* Update README.md to 1.4.0cuba13.1.1 for dorado

* Update README.md updated to the current models

* Create README.md for 1.4.0-cuba13.1.1-no_model

* Create Dockerfile for 1.4.0 cuba no model

* Update README.md for 1.4.0cuba13.1.1-no_model dorado

* Update README.md fix the link

* Update README.md back to old Cuda

Removing this: 13.1.1 is preferred.

* Update Dockerfile updated back to Cuda 12.2

* Rename dorado folder back to 1.4.0-cuda12.2.0

* Update Dockerfile all the way back

nvidia/cuda:12.2.0-base-ubuntu22.04

* Update README.md back to old cuda

Removed the line 13.1.1 is preferred.

* Update Dockerfile to go back to old cuda

Added: nvidia/cuda:12.2.0-base-ubuntu22.04

* Update Dockerfile

* Rename dorado folder back to 1.4.0-cuda12.2.0-no_model

* Update README.md to cuda 12.2.0

* Update README.md updated the models details

* Update README.md correcting my packages

* Fix Docker run command for CUDA 12.2.0

Updated the README to reflect the correct Docker image tag for CUDA 12.2.0.

* Delete build-files/dorado/1.1.0-cuda12.2.0/README.md

accidental change in PR

---------

Co-authored-by: Kutluhan Incekara <46578029+Kincekara@users.noreply.github.com>

Author: cwoodside1278

README.md

@@ -156,7 +156,7 @@ 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) | <details><summary>Click to see all versions</summary> <ul><li>[0.6.2](./build-files/datasets-sars-cov-2/0.6.2/)</li><li>[0.6.3](./build-files/datasets-sars-cov-2/0.6.3/)</li><li>[0.7.2](./build-files/datasets-sars-cov-2/)</li></ul> </details> | https://github.com/CDCgov/datasets-sars-cov-2 |
 | [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.0](./build-files/dnaapler/0.1.0/)</li></ul> <ul><li>[0.4.0](./build-files/dnaapler/0.4.0/)</li><li>[0.5.0](./build-files/dnaapler/0.5.0/)</li><li>[0.5.1](./build-files/dnaapler/0.5.1/)</li><li>[0.7.0](./build-files/dnaapler/0.7.0/)</li><li>[0.8.0](./build-files/dnaapler/0.8.0/)</li><li>[1.0.1](./build-files/dnaapler/1.0.1/)</li><li>[1.1.0](./build-files/dnaapler/1.1.0/)</li><li>[1.2.0](./build-files/dnaapler/1.2.0/)</li><li>[1.3.0](./build-files/dnaapler/1.3.0/)</li></ul> </details> | https://github.com/gbouras13/dnaapler |
 | [diamond](https://github.com/bbuchfink/diamond) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/diamond)](https://hub.docker.com/r/staphb/diamond) | <details><summary>Click to see all versions</summary> <ul><li>[2.1.9](./build-files/diamond/2.1.9)</li><li>[2.1.10](./build-files/diamond/2.1.10)</li><li>[2.1.11](./build-files/diamond/2.1.11)</li><li>[2.1.12](./build-files/diamond/2.1.12)</li><li>[2.1.13](./build-files/diamond/2.1.13)</li><li>[2.1.16](./build-files/diamond/2.1.16)</li><li>[2.1.22](./build-files/diamond/2.1.22)</li><li>[2.1.23](./build-files/diamond/2.1.23)</li></ul> </details> | https://github.com/bbuchfink/diamond|
-| [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.8.0](./build-files/dorado/0.8.0/)</li><li>[0.8.3](./build-files/dorado/0.8.3/)</li><li>[0.9.0](./build-files/dorado/0.9.0-cuda12.2.0/)</li><li>[0.9.0-cuda12.2.0-no_model](./build-files/dorado/0.9.0-cuda12.2.0-no_model/)</li><li>[1.1.0-cuda12.2.0](./build-files/dorado/1.1.0-cuda12.2.0/)</li><li>[1.1.0-cuda12.2.0-no_model](./build-files/dorado/1.1.0-cuda12.2.0-no_model/)</li></ul></ul> </details> | [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.8.0](./build-files/dorado/0.8.0/)</li><li>[0.8.3](./build-files/dorado/0.8.3/)</li><li>[0.9.0](./build-files/dorado/0.9.0-cuda12.2.0/)</li><li>[0.9.0-cuda12.2.0-no_model](./build-files/dorado/0.9.0-cuda12.2.0-no_model/)</li><li>[1.1.0-cuda12.2.0](./build-files/dorado/1.1.0-cuda12.2.0/)</li><li>[1.1.0-cuda12.2.0-no_model](./build-files/dorado/1.1.0-cuda12.2.0-no_model/)</li><li>[1.4.0-cuda12.2.0](./build-files/dorado/1.4.0-cuda12.2.0/)</li><li>[1.4.0-cuda12.2.0-no_model](./build-files/dorado/1.4.0-cuda12.2.0-no_model/)</li></ul></ul> </details> | [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) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.14](./build-files/dragonflye/1.0.14/)</li><li>[1.1.1](./build-files/dragonflye/1.1.1/)</li><li>[1.1.2](./build-files/dragonflye/1.1.2/)</li><li>[1.2.0](./build-files/dragonflye/1.2.0/)</li><li>[1.2.1](./build-files/dragonflye/1.2.1/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.1](./build-files/drprg/0.1.1/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[0.0.100](./build-files/dsk/0.0.100/)</li><li>[2.3.3](./build-files/dsk/2.3.3/)</li></ul> </details> | https://gatb.inria.fr/software/dsk/ |

build-files/dorado/1.1.0-cuda12.2.0/README.md

@@ -0,0 +1,36 @@
+FROM nvidia/cuda:12.2.0-base-ubuntu22.04 AS app
+
+ARG DORADO_VER="1.4.0"
+
+LABEL base.image="nvidia/cuda:12.2.0-base-ubuntu22.04"
+LABEL dockerfile.version="1"
+LABEL software="Dorado"
+LABEL software.version="${DORADO_VER}"
+LABEL description="A tool for basecalling Fast5/Pod5 files from Oxford Nanopore sequencing"
+LABEL website="https://github.com/nanoporetech/dorado"
+LABEL license="https://github.com/nanoporetech/dorado/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluhan.incekara@ct.gov"
+
+RUN apt-get update && apt-get install --no-install-recommends -y\
+    wget \
+    ca-certificates \
+    pigz \
+    procps &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget -q https://cdn.oxfordnanoportal.com/software/analysis/dorado-${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
+
+RUN wget https://github.com/nanoporetech/dorado/raw/release-v1.1/tests/data/pod5/dna_r10.4.1_e8.2_400bps_5khz/dna_r10.4.1_e8.2_400bps_5khz-FLO_PRO114M-SQK_LSK114_XL-5000.pod5 &&\
+    dorado basecaller fast dna_r10.4.1_e8.2_400bps_5khz-FLO_PRO114M-SQK_LSK114_XL-5000.pod5

build-files/dorado/1.4.0-cuda12.2.0-no_model/Dockerfile

@@ -0,0 +1,33 @@
+# Dorado 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. The models can be downloaded manually by `dorado download` command. If no specific model is provided, Dorado will automatically select and download the appropriate one using the model selection complex.
+- Cuda drivers >= 12.2.0 are required for gpu support.
+- Use **"--gpus all"** flag to activate gpu support in docker. E.g.
+`docker run -it --gpus all staphb/dorado:1.4.0-cuda13.1.1-no_model bash`
+- Support for Fast5 files and basecalling models for DNA R10.4.1 4kHz data, DNA R9.4.1, and RNA002 were removed after v0.9.6
+
+Full documentation: https://dorado-docs.readthedocs.io/en/latest/
+
+## Example Usage
+```bash
+# list models
+dorado download --list
+# download a single model
+dorado download --model {model_name}
+# download all models
+dorado download
+# basecaller
+dorado basecaller {model} {data} > calls.bam
+```

build-files/dorado/1.4.0-cuda12.2.0-no_model/README.md

@@ -0,0 +1,60 @@
+# Use NVIDIA CUDA image as the base image
+FROM nvidia/cuda:12.2.0-base-ubuntu22.04 AS app
+
+ARG DORADO_VER="1.4.0"
+
+# Metadata
+LABEL base.image="nvidia/cuda:12.2.0-base-ubuntu22.04"
+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"
+
+# Install dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    curl \
+    ca-certificates \
+    pigz && \
+    rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+# Download and extract Dorado package
+RUN wget -q 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
+
+# Set environment variables
+ENV LC_ALL=C
+
+# Download basecalling models
+RUN mkdir /dorado_models && \
+    cd /dorado_models && \
+    dorado download --model all
+
+# Default command
+CMD ["dorado", "-h"]
+
+WORKDIR /data
+
+# -----------------------------
+# Test Stage
+# -----------------------------
+FROM app AS test
+
+# Download the specific Pod5 test file
+RUN wget https://github.com/nanoporetech/dorado/raw/release-v1.1/tests/data/pod5/dna_r10.4.1_e8.2_400bps_5khz/dna_r10.4.1_e8.2_400bps_5khz-FLO_PRO114M-SQK_LSK114_XL-5000.pod5
+
+# Run test command (using CPU mode)
+RUN dorado basecaller \
+    --device cpu \
+    /dorado_models/dna_r10.4.1_e8.2_400bps_sup@v5.2.0 \
+    dna_r10.4.1_e8.2_400bps_5khz-FLO_PRO114M-SQK_LSK114_XL-5000.pod5 \
+    --emit-moves --max-reads 10 > basecalled.sam
+
+# Verify the output file exists and is not empty
+RUN test -s basecalled.sam