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Getting Started

Installation

Sopa package

Sopa can be installed on every OS with pip or poetry.

The preferred Python version is python==3.10, but we also support 3.11 and 3.12.

Advice (optional)

We advise creating a new environment via a package manager (except if you use Poetry, which will automatically create the environment).

For instance, you can create a new conda environment:

conda create --name sopa python=3.10
conda activate sopa

Choose one of the following, depending on your needs (it should take at most a few minutes):

pip install sopa

To install extras (for example, if you want to use cellpose/baysor), please run:

# choose any valid extra among cellpose/baysor/tangram/wsi
pip install 'sopa[cellpose,baysor]'

git clone https://github.com/gustaveroussy/sopa.git
cd sopa

# no extra
pip install  -e .

# or, to install extras, among cellpose/baysor/tangram/wsi:
pip install -e '.[cellpose,baysor]'

git clone https://github.com/gustaveroussy/sopa.git
cd sopa

poetry install --all-extras

Baysor usage

Even though pip install 'sopa[baysor]' will install some dependencies related to baysor, you still have to install the baysor command line (see the official documentation) if you want to use it.

If the Baysor executable is not at ~/.julia/bin/baysor, please make the baysor command available (e.g., via creating a symlink ~/.local/bin/baysor pointing to executable), or export the path to the executable via export baysor=/path/to/baysor/executable.

Snakemake setup

To use Snakemake, in addition to the above sopa environment, you'll need to clone a repository containing the Snakemake workflow:

git clone https://github.com/gustaveroussy/sopa.git
cd sopa   # move inside the sopa repository

Also, make sure you have installed snakemake>=8.0.0. This does not necessarily have to be inside the sopa environment: for instance, you can create a new environment specific to snakemake:

# this will create a new environment called "snakemake"
conda create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

Now, follow our snakemake tutorial to run your first pipeline.

Usage

Sopa comes in three different flavours, each corresponding to a different use case:

  • API: use directly sopa as a Python package for full flexibility and customization (see a tutorial here)
  • Snakemake pipeline: choose a config, and run our pipeline on your spatial data in a few minutes. See our snakemake tutorial.
  • CLI: use our command-line-interface to prototype quickly your own pipeline