SetupPrscsRule

Reactive rule that creates the PRS-CS Python environment. A single prscs resource couples both components:

• A Python venv with numpy, scipy, and h5py installed.
• A git clone of the PRS-CS repository providing the helper modules (gigrnd.py, parse_genet.py, mcmc_gtb.py) imported by the PolyGenius PRS-CS wrapper in inst/python/polygenius_prscs.py.

The stored resource data is list(python = <venv python3>, source = <clone dir>).

PRS-CS environment setup rule

PolyGenius::Rule -> SetupPrscsRule

Public methods

• SetupPrscsRule$new()
• SetupPrscsRule$matches()
• SetupPrscsRule$inputs()
• SetupPrscsRule$requirements()
• SetupPrscsRule$run()

Method new()

Create the rule.

Usage

SetupPrscsRule$new()

Method matches()

Check whether this rule produces the requested output.

Usage

SetupPrscsRule$matches(output.spec)

Arguments

output.spec — Output resource specification.

Returns

TRUE for a prscs output.

Method inputs()

Declare upstream inputs.

Usage

SetupPrscsRule$inputs(output.spec)

Arguments

output.spec — Output resource specification.

Returns

An empty list; the rule has no inputs.

Method requirements()

Declare resource requirements.

Usage

SetupPrscsRule$requirements(output.spec, inputs)

Arguments

output.spec — Output resource specification.

inputs — Bound input values.

Returns

Named list with cores and memory.

Method run()

Resolve the resource.

Usage

SetupPrscsRule$run(output.spec, inputs, logger = pg.logger())

Arguments

output.spec — Output resource specification.

inputs — Named list of bound input values.

logger — Rule logger.

Returns

Rule result list with data, meta and logs.

Rule

Other setup-rules: ResolveGctbRule, ResolvePlinkRule, SetupBigsnprRule, SetupLiftoverRule