Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix singularity config #208

Merged
merged 2 commits into from
Feb 21, 2025
Merged

Fix singularity config #208

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
5bd29fa
fix singularity config
luisas Feb 21, 2025
439a33c
fix lint
luisas Feb 21, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 4 additions & 6 deletions nextflow.config
View file
Open in desktop
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