Commit b422bb46 authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Improve Setup section with detailed description of mlpy installation

parent 0b30429c
### Integrative Network Fusion (INF)
# Integrative Network Fusion (INF)
![INF pipeline ](figs/INF_pipeline.jpeg)
**Setup**
## Setup
```bash
git clone https://gitlab.fbk.eu/MPBA/INF
cd INF
......@@ -9,19 +9,44 @@ conda env create -f env.yml -n inf
conda activate inf
```
### Additional dependencies
#### R dependencies
To install the R dependencies (not in conda channels), run the following command via the R prompt:
```bash
install.packages("TunePareto")
```
To install `mlpy`, follow the instructions [here](https://gitlab.fbk.eu/MPBA/mlpy).
#### MLPY
To install `mlpy` follow this instructions:
`mlpy` package is required for some operations included in the DAP procedure.
The `mlpy` package available on PyPI is outdated and not working on OSX platforms.
These are the steps to follow:
Let `<ANACONDA>` be your anaconda path (e.g., `/home/user/anaconda3`).
Adjust these environmental variables:
```bash
export LD_LIBRARY_PATH=<ANACONDA>/envs/<ENV>/lib:${LD_LIBRARY_PATH}
export CPATH=<ANACONDA>/envs/<ENV>/include:${CPATH}
```
and then install `mlpy` from GitLab:
```bash
pip install git+https://gitlab.fbk.eu/MPBA/mlpy.git
```
#### Other Python dependencies
To install `bootstrapped`:
```bash
pip install bootstrapped
```
## Usage
**Input files**
* omics layer 1 data: samples x features, tab-separated, with row & column names
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment