# Installation and Usage

## Install Oris

Dependencies: `Python 3.10+`, `boolevard`, `mpi4py`, `pandas`, `numpy`, `multiprocessing`.

> 📝 **Note:** Oris is designed to run on high-performance computing (HPC) systems equipped with:
>
> * SLURM workload manager for job scheduling
> * An MPI implementation (e.g. OpenMPI or Intel MPI)
> * `Python 3.10+` and `mpi4py`

To install Oris, run the following command:

```
pip install git+https://github.com/druglogics/oris.git
```

## Quick Start

To execute Oris, a minimal invocation is:

```
oris --zips /path/to/zips --sampling 10 --mode synergies
```

Oris requires three mandatory parameters: `--zips`, `--sampling`, and  `--mode`. The `--zips` parameter specifies the directory containint the ZIP files with the expecter internal structure (see [*Helpers*](helpers.md)). The `--sampling` parameter defiens how many models are selected from the Gitsbe-generated ensemble (see [*Sampling*](sampling.md)). Finally, the `--mode` parameter controls the operational mode of Oris, which can be set to `synergies`, `countpaths`, or `full` (see [*Oris Modes*](orismodes.md)).

Oris always operates using a configuration file (see [*Configuration*](configuration.md)). If no configuration file is explicitly provided via the optional `--config` parameter, Oris automatically falls back to a default configuration.

## Outputs

Oris produces outputs by augmenting the same ZIP files provided as input with an additional directory named Results. The specific contents of this directory depend on the selected operating mode (see [*Oris Modes*](orismodes.md)):

- `synergies`: writes  `PathCounts` and `SynergyExcess` files .
- `countpaths`: writes a `PathCountsFull` file.
- `full`: writes  `PathCounts`, `PathCountsFull`, and `SynergyExcess` files.