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Cluster setup
You can run the workflow either on a cluster setup or on you local machine.
For local runs no further configuration is required except for running the snakemake commands with the --cores N flag, where N is the number of cores you want to allocate.
If you want to run the workflow on a cluster you need to configure the submission of the cluster runs in a profile.
An example profile is provided in $HOME/graph-concept-learner/workflows/profile. Adding the following to your $HOME/.bashrc will enable cluster execution:
export SNAKEMAKE_PROFILE=$HOME/graph-concept-learner/workflows/profileThe workflow supports SLURM and LSF batch systems. Users must specify in $HOME/graph-concept-learner/workflows/profile/config.yaml which one will be used.
For LSF in $HOME/graph-concept-learner/workflows/profile/config.yaml:
# Specify custom job submission wrapper
cluster: "../scripts/LSF_cluster_job.py"For SLURM:
# Specify custom job submission wrapper
cluster: "../scripts/SLURM_cluster_job.py"
# Specify custom job status command wrapper
cluster-status: "../scripts/SLURM_cluster_status.py"