= Network Inference Pipeline

This project uses the https://github.com/drostlab/network-inference-toolbox[Network Inference Toolbox], a collection of Singularity containers packaging various pre-existing tools for Gene Regulatory Network Inference, to infer and evaluate some networks for specific datasets.


== Dependencies

* https://www.python.org/[Python] v3.9 with https://python-poetry.org/[Poetry] set up
* https://sylabs.io/[Singularity] (tested with v3.7)
* `git` (optional)


== Overview

This project is a https://dvc.org/[DVC] pipeline that glues data preprocessing, tools from `toolbox/bin` and network evaluation together. After setup as described below, you should be able to `dvc repro` the results.

NOTE: To package up materials used for the https://doi.org/10.1101/2021.01.17.427026[`noisyR` paper] (Moutsopoulos et al.), run `dvc repro artifacts/noisyR-paper/dvc.yaml`, which will also implicitly generate its dependencies. The resulting tarball will be placed in `artifacts/noisyR-paper`.


== Setup

Clone (or download and extract) this repository and enter its directory. You then need to setup both Python dependencies and the previously mentioned Network Inference Toolbox.


=== Python Dependencies

The recommended (but optional) way to setup DVC is to install it into a virtual environment. (E.g., call `poetry shell` and then always run `dvc` from there.) Then just run `poetry install`.


=== Network Inference Toolbox

The recommended way to setup the Toolbox is to pull the Git submodule. In the repository root, execute:

[source,sh]
----
git submodule init
git submodule update
----

After setting up the submodule, you can build the containers by entering the `toolbox` directory and then running `make` (or, if the containers were already built somewhere else, just copy them to `toolbox/bin`).

The only parts of the Network Inference Toolbox that are strictly necessary to run the pipeline are the assembled Singularity containers (i.e. `.sif` files), which the pipeline expects to find in `toolbox/bin`. If you are sure you just want to _run_ the pipeline (and not change it), you alternatively could copy the containers there, or symlink `toolbox/bin` to another location where the containers are available, without setting up the submodule as described above.