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Sanger profile update

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This commit is contained in:
Priyanka Surana 2022-07-20 13:14:42 +01:00
parent a02bd46617
commit 58508c4fbc
1 changed files with 22 additions and 24 deletions
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34
conf/sanger.config
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@ -1,25 +1,19 @@
// Profile details
params { params {
config_profile_description = 'The Wellcome Sanger Institute HPC cluster profile' config_profile_description = 'The Wellcome Sanger Institute HPC cluster (farm5) profile'
config_profile_contact = 'Anthony Underwood (@aunderwo)' config_profile_contact = 'Priyanka Surana (@priyanka-surana)'
config_profile_url = 'https://www.sanger.ac.uk/group/informatics-support-group/' config_profile_url = 'https://www.sanger.ac.uk'
}
singularity {
enabled = true
cacheDir = "${baseDir}/singularity"
runOptions = '--bind /lustre --bind /nfs/pathnfs01 --bind /nfs/pathnfs02 --bind /nfs/pathnfs03 --bind /nfs/pathnfs04 --bind /nfs/pathnfs05 --bind /nfs/pathnfs06 --no-home'
} }
// Queue and retry strategy
process{ process{
executor = 'lsf' executor = 'lsf'
queue = 'normal' queue = { task.time < 12.h ? 'normal' : task.time < 48.h ? 'long' : 'basement' }
errorStrategy = { task.attempt <= 5 ? "retry" : "finish" } errorStrategy = 'retry'
process.maxRetries = 5 maxRetries = 5
withLabel:process_long {
queue = 'long'
}
} }
// Executor details
executor{ executor{
name = 'lsf' name = 'lsf'
perJobMemLimit = true perJobMemLimit = true
@ -28,8 +22,12 @@ executor{
killBatchSize = 50 killBatchSize = 50
} }
// Max resources
params { params {
max_memory = 128.GB max_memory = 683.GB
max_cpus = 64 max_cpus = 256
max_time = 48.h max_time = 720.h
} }
// For singularity
singularity.runOptions = '--bind /lustre --bind /nfs'