Installation

CHART is a Python package (Python ≥ 3.9) that installs the chart command. Some parts of the pipeline need more than the package itself.

Component	Needed for	Install
CHART	every stage	pip install .
R 4.5 and its packages	chart archetypes, every step but pca and crops	environment.yml
scallops	the crops step of chart archetypes; the pheno and pheno_sbs QC components	pip install scallops
annotation extra	chart annotation	pip install ".[annotation]"
fsspec and a filesystem driver	inputs or outputs on remote storage	pip install fsspec s3fs for S3

CHART

git clone https://github.com/Genentech/CHART.git
cd CHART
pip install .

R

All steps of chart archetypes except pca and crops are R scripts, which the stage runs with Rscript. environment.yml describes a conda environment, chart-r, with R 4.5 and the packages the scripts load. The archetypes package is on CRAN but not conda-forge, so it is installed separately:

mamba env create -f environment.yml
conda activate chart-r
Rscript -e 'install.packages("archetypes", repos="https://cloud.r-project.org")'

Rscript must be on PATH when chart archetypes runs, for instance with chart-r activated alongside the Python environment holding CHART. Before its first step, the stage checks that R can load every package the scripts need, and names any it cannot. The compiled packages, r-supercell in particular, are built for one R minor version, which is why the environment fixes R to 4.5.

scallops

scallops reads the registered images. Without it, CHART skips the components that need images, with a warning: the crops of archetypal cells, and the phenotype-correlation QC components. An explicit request for one of them, --steps crops or --components pheno, fails instead. scallops requires Python ≥ 3.12.

Annotation

chart annotation describes archetypes from their crops with a multimodal language model. Its packages are an optional extra:

pip install ".[annotation]"

The model is set by annotation.model in the config, gpt-5.5 by default. Credentials are read from the environment only. Two providers are supported:

Provider	Variables
OpenAI-compatible gateway, such as LiteLLM	LITELLM_API_KEY and LITELLM_BASE_URL; OPENAI_API_KEY and OPENAI_BASE_URL are also accepted, and OPENAI_API_KEY alone addresses OpenAI itself
Azure OpenAI	AZURE_OPENAI_API_KEY and AZURE_OPENAI_ENDPOINT; optionally AZURE_OPENAI_API_VERSION, and AZURE_DEPLOYMENT_MAP where deployment names differ from model names, e.g. '{"gpt-5.5": "gpt-5-5-deploy"}'

LLM_PROVIDER selects gateway, azure or auto; auto, the default, uses the gateway when its variables are set and Azure otherwise.

Remote storage

Paths in the config may point to remote storage, such as s3:// URLs. Reading and writing them needs fsspec and the driver for the filesystem, s3fs for S3, which are not installed with CHART.