External Tools and Environment

CREDTOOLS is a Python package, but some workflows call external programs. You only need the tools used by your chosen path.

What You Need

Workflow	Extra tools
munge only	none beyond Python dependencies
chunk with LD extraction	plink on PATH
finemap --tool susie	none beyond Python dependencies
finemap --tool finemap	finemap executable
finemap --tool susiex	SuSiEx executable
finemap --tool susie_ash or susie_inf	Rscript and susieR >= 0.16.1
finemap --tool carma	Rscript and R package CARMA
finemap --tool mesusie	Rscript and R package MESuSiE

Install only what you use

A basic SuSiE run does not need R, FINEMAP, or SuSiEx. Add specialized tools after the core workflow works on your machine.

Python Environment

CREDTOOLS supports Python >=3.9,<3.13.

python -m pip install credtools
credtools --version
credtools --help

For local development:

uv sync
uv run pytest

PLINK

credtools chunk uses PLINK when ld_ref is present in the population config. The reference prefix must point to .bed, .bim, and .fam files:

popu    cohort  sample_size path    ld_ref
EUR UKBB    400000  work/munged/EUR_UKBB.munged.txt.gz  /ref/1kg/EUR

Check PLINK first:

plink --version
ls /ref/1kg/EUR.bed /ref/1kg/EUR.bim /ref/1kg/EUR.fam

CREDTOOLS currently supports PLINK LD extraction. VCF LD extraction is not implemented.

FINEMAP and SuSiEx Executables

CREDTOOLS resolves executable paths in this order:

1. a custom path set in Python with tool_manager.set_tool_path(...),
2. the system PATH,
3. the bundled credtools/bin/<tool> path, if present.

For CLI usage, the most practical option is to put the executable on PATH:

which finemap
finemap --help

which SuSiEx
SuSiEx --help

On a cluster, load the module before running CREDTOOLS:

module load finemap
module load plink
credtools pipeline loci_list.txt results --tool finemap

R-Based Tools

Check R:

Rscript --version

For SuSiE-ash and SuSiE-inf:

Rscript -e 'library(susieR); packageVersion("susieR")'

The wrapper expects a SuSiE 2.0 capable susieR with support for unmappable_effects. If the installed package is too old, upgrade susieR.

For CARMA:

install.packages("devtools")
devtools::install_github("ZikunY/CARMA")

For MESuSiE:

install.packages("devtools")
devtools::install_github("borangao/MESuSiE")

Temporary Files

Some wrappers write intermediate files under ./tmp/:

Tool	Temporary parent directory
FINEMAP	./tmp/FINEMAP
SuSiEx	./tmp/SuSiEx
MESuSiE	./tmp/MESuSiE

Normal runs clean these folders after each tool call. Debug-level logging may keep temporary directories so you can inspect tool inputs and logs.

Quick Environment Test

Run a tiny smoke test before a large job:

credtools pipeline test_loci_list.txt smoke_results \
  --tool susie \
  --max-causal 2 \
  --log-file smoke.log

If the smoke test fails, fix the environment or schema first. Do not submit the full batch and hope the cluster logs are easier to read.