Singularity container?

[YichaoOU]

Hello,

Our HPC can't run docker applications.

Is this possible that you can make a singularity container?

Thank you! Yichao

[adeslatt]

Yes. This is quite easily done. If you run on premise with an executor such as Slurm -- you can see how to do something by using the explanations on the Jackson Laboratory Alternative Splicing Pipeline workflow here. Using the config file for running on sumner (the name of the on premise HPC) https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/master/conf/executors/sumner.config and how to use singulatory -- assumed by sumner https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/master/conf/executors/singularity.config

[YichaoOU]

Thanks!

[YichaoOU]

Usually in nf-core, you can directly add -profile singularity, but it seems this can not be used here? because I got this error:

nextflow run main.nf --config conf/test_with_sqanti.config -profile singularity

Unknown configuration profile: 'singularity'

Thanks, Yichao

[adeslatt]

Hi @YichaoOU , I always like to remind people that there is no magic in programming. The nf-core community has a defined profile for the option in a workflow that allows you to specify -profile singularity. If you look here at the sarek workflow https://github.com/nf-core/sarek/blob/master/nextflow.config you will see that there is a profile called singularity. We can add this as a feature request or you can modify your own nextflow.config file to have the same.

Code permalink

Code snippet here:

profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }
    conda {
        params.enable_conda    = true
        charliecloud.enabled   = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        singularity.enabled    = false
    }
    mamba {
        conda.useMamba         = true
        params.enable_conda    = true
        charliecloud.enabled   = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        singularity.enabled    = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = { params.use_gatk_spark ? false : true }.call()
        charliecloud.enabled   = false
        podman.enabled         = false
        shifter.enabled        = false
        singularity.enabled    = false
    }
    singularity {
        singularity.autoMounts = true
        singularity.enabled    = true
        charliecloud.enabled   = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
    }
    podman {
        podman.enabled         = true
        charliecloud.enabled   = false
        docker.enabled         = false
        shifter.enabled        = false
        singularity.enabled    = false
    }
    shifter {
        shifter.enabled        = true
        charliecloud.enabled   = false
        docker.enabled         = false
        podman.enabled         = false
        singularity.enabled    = false
    }
    charliecloud {
        charliecloud.enabled   = true
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        singularity.enabled    = false
    }
    gitpod {
        executor.cpus          = 16
        executor.memory        = 60.GB
        executor.name          = 'local'
    }

If you would like, you can create an issue as a code improvement and we will add it as we can. It isn't a bad suggestion - but shouldn't hold you up as you can adjust yours to do the same. If you make a pull request with the change we can merge it after testing. Cheers!