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Support Singularity successor Apptainer (Cannot enable more than one container engine -- Choose either one of: singularity, apptainer) #8

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paulmenzel opened this issue Mar 22, 2023 · 1 comment
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Support Singularity successor Apptainer (Cannot enable more than one container engine -- Choose either one of: singularity, apptainer) #8

paulmenzel opened this issue Mar 22, 2023 · 1 comment
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enhancement New feature or request

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@paulmenzel
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SIMPLI/nextflow.config

Lines 1 to 3 in 09e3bd4

singularity.enabled = true
singularity.autoMounts = true
singularity.cacheDir = "singularity/containers"

Apptainer is the successor of Singularity.

$ curl https://singularity.hpcng.org/
<!DOCTYPE html>
<html>             
    <head>
        <meta http-equiv="refresh" content="0; url='https://apptainer.org/index.html'" />
    </head>
    <body>
        <h2 style="text-align: center; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;">This page has been moved to our new domain! ( apptainer.org ). Please wait well we redirect you. </h2>
[…]

Nextflow supports a variety of container runtimes, including Apptainer. It’d be nice, if SIMPLI would support it too and not hardcode Singularity.

$ ./launch.sh run https://github.com/ciccalab/SIMPLI -profile test -with-apptainer /dev/shm/nextflow/singularity/containers/simpli_imaging-default-simpli_imctools_stardist-test.img
N E X T F L O W  ~  version 23.02.1-edge
Launching `https://github.com/ciccalab/SIMPLI` [condescending_dalembert] DSL2 - revision: 09e3bd432a [master]
Cannot enable more than one container engine -- Choose either one of: singularity, apptainer
@MicheleBortol
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MicheleBortol commented Mar 26, 2023 •
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Hi @paulmenzel,

Thank you for pointing this out it is a good suggestion. I updated the nextflow.config file to support both apptainer and singularity. See e9fc4f1 for details. To run the pipeline now you need to specify either apptainer or singularity as a profile. For instance:

  • nextflow run ciccalab/SIMPLI -profile test,singularity
  • nextflow run ciccalab/SIMPLI -profile test,apptainer
    Using the -with--aptainer option is not possible because SIMPLI depends on 3 separate containers.

Please let me know if this works for you.

Best wishes

Michele

@MicheleBortol MicheleBortol added the enhancement New feature or request label Mar 29, 2023
@MicheleBortol MicheleBortol mentioned this issue Mar 29, 2023
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@paulmenzel @MicheleBortol