README.md

# masterJLU2018

De novo motif discovery and evaluation based on footprints identified by TOBIAS

## Dependencies
* [conda](https://conda.io/docs/user-guide/install/linux.html)
* [Nextflow](https://www.nextflow.io/)
* [MEME-Suite](http://meme-suite.org/doc/install.html?man_type=web)

## Installation
Start with installing all dependencies listed above.
Download all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018). 
The Nextflow-script needs a conda enviroment to run. To create this enviroment you need the yml-file from the repository.
Run the following commands to create the enviroment:
```console
path=[Path to given masterenv.yml file]
conda env create --name masterenv -f=$path
source activate masterenv
```

## Quick Start
```console
nextflow run pipeline.nf --input [INPUT-file] --bed [INPUT-bed] --genome_fasta [path to file] --jaspar_db [path to motif database as meme-file] --config uropa.config
```
## Parameter

For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki)