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Fix singularity config #208

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Merged
luisas merged 2 commits into from
Feb 21, 2025
Merged

Fix singularity config #208

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5bd29fa
fix singularity config
luisas Feb 21, 2025
439a33c
fix lint
luisas Feb 21, 2025
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10 changes: 4 additions & 6 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -123,22 +123,21 @@ profiles {
}
docker {
docker.enabled = true
docker.runOptions = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)'
docker.runOptions = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)'
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64'
docker.runOptions = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
singularity.runOptions = params.use_gpu ? '--nv' : singularity.runOptions
singularity.runOptions = params.use_gpu ? '--nv' : ""
conda.enabled = false
docker.enabled = false
podman.enabled = false
Expand Down Expand Up @@ -177,7 +176,7 @@ profiles {
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
apptainer.runOptions = params.use_gpu ? '--nv' : apptainer.runOptions
apptainer.runOptions = params.use_gpu ? '--nv' : ""
conda.enabled = false
docker.enabled = false
singularity.enabled = false
Expand Down Expand Up @@ -236,7 +235,6 @@ charliecloud.registry = 'quay.io'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
Expand Down