Configure your HPC cluster once and reuse it for every project. This builds a Nextflow config from a generic scheduler template, fills in the cluster-level settings you provide (queue, account / clusterOptions, container engine), and saves it as a named profile in [mitopilot_config_dir()]. Afterwards, `new_project(executor = "<name>")` (or `new_project_userAsmb()`) will find and use it automatically, filling in the remaining per-project values.
Usage
generate_config(
name,
scheduler = c("slurm", "sge", "pbs", "lsf", "local", "awsbatch", "NMNH_Hydra",
"NOAA_SEDNA"),
container_engine = c("auto", "singularity", "apptainer", "docker", "none"),
container_cache = NULL,
container_run_options = NULL,
native_prefix = NULL,
queue = NULL,
account = NULL,
cluster_options = NULL,
penv = "mthread",
profile_dir = mitopilot_config_dir(),
interactive = FALSE,
overwrite = FALSE
)Arguments
- name
Profile name. Saved as `config.<name>`; pass this as the `executor` argument to `new_project()`.
- scheduler
Base template to build on. One of "slurm", "sge", "pbs", "lsf", "local", or "awsbatch"; or a named cluster template ("NMNH_Hydra", "NOAA_SEDNA"), allowed only with `container_engine = "none"`, which keeps that cluster's tuned resource settings and swaps its container block for the native install.
- container_engine
Container runtime. "auto" picks docker for local/awsbatch and singularity for HPC schedulers; or set explicitly to "singularity", "apptainer", or "docker"; or "none" for a native (no-container) install built by inst/native/install_mitopilot_native.sh, which requires native_prefix.
- container_cache
Optional cacheDir for singularity/apptainer.
- container_run_options
Optional runOptions for singularity/apptainer (e.g. bind mounts).
- native_prefix
Directory passed to `install_mitopilot_native.sh –prefix` (contains `activate.sh` and `ref_dbs/`). Required when `container_engine = "none"`, ignored otherwise.
- queue
Partition / queue name. If `NULL`, the queue directive is omitted (cluster default is used).
- account
Optional accounting / project string. Folded into clusterOptions per scheduler (SLURM `–account=`, PBS `-A`, LSF `-P`, SGE `-P`).
- cluster_options
Optional raw clusterOptions string appended verbatim.
- penv
SGE parallel environment (default "mthread"); ignored for other schedulers.
- profile_dir
Directory to save the profile in (default [mitopilot_config_dir()]).
- interactive
If `TRUE` and running interactively, prompt for any unset queue / account / cluster_options / container values.
- overwrite
Overwrite an existing profile of the same name (default `FALSE`).