Commit 4296736a authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Add environment file

parent 0dda140d
### INF pipeline
**Requirements**
Python3 with mlpy (!), numpy, scikit-learn, pandas, snakemake
R >= 3.2.3 with argparse, cvTools, doParallel, TunePareto, igraph, lubridate, data.table
To install R via Anaconda: [doc](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/)
**Setup**
```bash
git clone https://gitlab.fbk.eu/MPBA/inf_revamped
cd inf_revamped
conda env create -f env.yml -n inf
conda activate inf
```
To install the R dependencies, run the following command from the R prompt:
To install the R dependencies (not in conda channels), run the following command via the R prompt:
```bash
install.packages("TunePareto")
```
`install.packages(c("argparse", "cvTools", "doParallel", "TunePareto", "igraph", "lubridate", "data.table"))`
To install mlpy, follow the instructions [here](https://gitlab.fbk.eu/MPBA/mlpy).
**Input files**
......
name: base
channels:
- defaults
- bioconda
dependencies:
- python=3.6
- gsl
- numpy
- scikit-learn
- libgcc
- r-cvtools
- r-doparallel
- r-igraph
- pandas
- r-argparse
- r-data.table
- r-lubridate
- matplotlib
- matplotlib-venn
- tqdm
- conda
- snakemake
prefix: //anaconda/envs/inf
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