Olamide Isreal
f776745722
- Update main.nf: Harbor container image, PVC mount paths, remove containerOptions and stageInMode - Update nextflow.config: Add k8s/k8s_gpu profiles, minimal config for WES injection - Update params.json: Correct paths for eureka PVC - Update Dockerfile.wes: CUDA base image for GPU support
56 lines
1.2 KiB
Plaintext
56 lines
1.2 KiB
Plaintext
manifest {
|
|
name = 'bioemu'
|
|
author = 'Olamide'
|
|
description = 'BioEmu - Biomolecular Emulator for protein structure sampling and binding energy analysis'
|
|
mainScript = 'main.nf'
|
|
version = '1.0.0'
|
|
}
|
|
|
|
params {
|
|
protein1_fasta = '/omic/eureka/bioemu/input/trp_cage.fasta'
|
|
protein2_fasta = '/omic/eureka/bioemu/input/villin_headpiece.fasta'
|
|
complex_name = 'protein_complex'
|
|
exp_dG = -10.0
|
|
outdir = '/omic/eureka/bioemu/output'
|
|
cache_dir = '/tmp/bioemu_cache'
|
|
num_samples = 10
|
|
batch_size = 5
|
|
temperature = 300
|
|
n_clusters = 5
|
|
}
|
|
|
|
profiles {
|
|
standard {
|
|
docker {
|
|
enabled = true
|
|
runOptions = '--gpus all'
|
|
}
|
|
}
|
|
|
|
k8s {
|
|
process {
|
|
executor = 'k8s'
|
|
}
|
|
docker {
|
|
enabled = true
|
|
}
|
|
}
|
|
|
|
k8s_gpu {
|
|
process {
|
|
executor = 'k8s'
|
|
pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
|
|
accelerator = [request: 1, type: 'nvidia.com/gpu']
|
|
}
|
|
docker {
|
|
enabled = true
|
|
}
|
|
}
|
|
}
|
|
|
|
process {
|
|
container = 'harbor.cluster.omic.ai/omic/bioemu:latest'
|
|
cpus = 2
|
|
memory = '8 GB'
|
|
}
|