Installation¶

Use Python 3.9, 3.10, 3.11, or 3.12.

Install CREDTOOLS¶

pipuvFrom source

python -m pip install credtools

uv pip install credtools

git clone https://github.com/Jianhua-Wang/credtools.git
cd credtools
python -m pip install -e ".[dev]"

Check that the command is available:

credtools --version
credtools --help

External Tools¶

Some fine-mapping engines need extra software. You only need to install the tools you plan to use.

Tool	Extra dependency	Notes
`susie`	none beyond Python dependencies	common default
`susie_ash`	R package `susieR >= 0.16.1`	adaptive shrinkage background
`susie_inf`	R package `susieR >= 0.16.1`	infinitesimal background
`finemap`	FINEMAP binary	binary is bundled in `credtools/bin`, but system installs are also supported
`carma`	R package `CARMA`	needs R
`mesusie`	R package for MESuSiE	needs R
`multisusie`	none beyond Python dependencies	best checked with a small run
`susiex`	SuSiEx binary/wrapper	needs method-specific setup

Start with the default

If you only want to verify the workflow, install CREDTOOLS and try --tool susie first. Add the more specialized tools after the basic path works on your machine.

For the full environment checklist, see External Tools and Environment.

R Setup¶

Several tools call R through Rscript. Check that it is available:

Rscript --version

Install common R packages:

install.packages(c("susieR", "ashr", "devtools"))

For CARMA:

devtools::install_github("ZikunY/CARMA")

Development Setup¶

For local development:

git clone https://github.com/Jianhua-Wang/credtools.git
cd credtools
uv sync
uv run pytest

If you are using pip instead of uv:

python -m pip install -e ".[dev]"
pytest

Common Install Problems¶

R package is installed but CREDTOOLS cannot find it

Make sure the same Rscript on your PATH can load the package:

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

External binary is not found

Run the command directly from your shell first. If your cluster uses modules, load the module before running CREDTOOLS.

Package installs but command is missing

Your Python environment may not be active. Run:

python -m pip show credtools
python -m pip install --upgrade credtools