Test docker container for Dorado

[Thomieh73]

Guppy is software for Nanopore technologies. To be able to use that in nextflow, I should make a complete container.

[Thomieh73]

apptainer can also use GPUs https://apptainer.org/docs/user/main/gpu.html#gpu-support-nvidia-cuda-amd-rocm

[Thomieh73]

I changed the title of this issue, set-up for Dorado

[Thomieh73]

Eve found that there is a docker container that can be used for Dorado.

https://hub.docker.com/r/nanoporetech/dorado

I will test if it is the right version and if it comes with the models or not

[Thomieh73]

The container was downloaded and test with these commands:
commands:

apptainer pull dorado_1.3.0.sif docker://nanoporetech/dorado

Then testing the container

apptainer exec dorado_1.3.0.sif dorado -v

or
apptainer run dorado_1.3.0.sif dorado -v

That works as expected. in both cases I got the correct version number.

Okay, that works, I will then try to make my pipeline run with containers.

[Thomieh73]

There is a new version of the dorado. check if that is here; https://hub.docker.com/r/nanoporetech/dorado/

[Thomieh73]

See these lines of code:

 conda (params.enable_conda ? "/cluster/projects/nn9305k/src/miniconda/envs/dorado_gpu_1.3.0" : null)
        container 'nanoporetech/dorado:shaf2aed69855de85e60b363c9be39558ef469ec365'

[Thomieh73]

and update the nextflow.config file with this block

// Define profiles
profiles {
    conda {
        params.enable_conda    = true
        apptainer.enabled      = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        apptainer.enabled      = false
        params.enable_conda    = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
 singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        apptainer.enabled      = false
        params.enable_conda    = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    podman {
        podman.enabled         = true
        apptainer.enabled      = false
        params.enable_conda    = false
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
shifter {
        shifter.enabled        = true
        apptainer.enabled      = false
        params.enable_conda    = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
    }
    charliecloud {
        charliecloud.enabled   = true
        apptainer.enabled      = false
        params.enable_conda    = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
    }
    apptainer {
        apptainer.enabled      = true
        apptainer.autoMounts   = true
        singularity.enabled    = false
        params.enable_conda    = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
}