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embl_hd: Add libraryDir and update executor configuration #1093

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Merged
fullama merged 3 commits into from
Apr 23, 2026
Merged

embl_hd: Add libraryDir and update executor configuration #1093

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2d6daca
Add libraryDir and update executor configuration
fullama Apr 22, 2026
d137c02
Merge branch 'master' into master
fullama Apr 22, 2026
3d8aaf8
Fix executor configuration for slurm
fullama Apr 22, 2026
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4 changes: 3 additions & 1 deletion conf/embl_hd.config
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ apptainer {
autoMounts = true
pullTimeout = "3 hours" // the default is 20 minutes and fails with large images
envWhitelist = 'CUDA_VISIBLE_DEVICES' // allow the bounding of GPU visible device variable into the containers
libraryDir = '/cvmfs/singularity.galaxyproject.org/all/'
}

singularity {
Expand Down Expand Up @@ -47,10 +48,11 @@ process {
}

executor {
name = "slurm"
$slurm {
queueSize = 200
submitRateLimit = "10/1sec"
pollInterval = '10sec'
exitReadTimeout = "5 min"
retry.reason = "*"
}
}
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