CLI Guide¶

Main commands¶

trait2gene run CONFIG
trait2gene validate CONFIG
trait2gene fetch-resources CONFIG
trait2gene run-magma CONFIG
trait2gene prep-features CONFIG
trait2gene run-pops CONFIG
trait2gene prioritize CONFIG
trait2gene report CONFIG
trait2gene inspect outputs PATH
trait2gene doctor

Recommended full-run flow¶

Before a production run:

trait2gene validate config.yaml
trait2gene doctor --config config.yaml
trait2gene fetch-resources config.yaml
trait2gene run config.yaml

Precomputed MAGMA flow¶

If .genes.out and .genes.raw already exist:

trait2gene validate config.precomputed.yaml
trait2gene run-pops config.precomputed.yaml
trait2gene prioritize config.precomputed.yaml
trait2gene report config.precomputed.yaml

`doctor`¶

doctor inspects environment and optional config wiring, including:

Python runtime basics
MAGMA reachability
cache and output writability
resolved resources when a config is supplied

`inspect outputs`¶

trait2gene inspect outputs PATH summarizes the standard output layout under a results directory and reports whether each expected section exists.