Commit 37d004e5 authored by peguerin's avatar peguerin
Browse files

update README

parent 1eae70dc
...@@ -6,7 +6,7 @@ Only_obitools pipeline using NEXTFLOW ...@@ -6,7 +6,7 @@ Only_obitools pipeline using NEXTFLOW
1. [Introduction](#1-introduction) 1. [Introduction](#1-introduction)
2. [Installation](#2-installation) 2. [Installation](#2-installation)
1. [Requirements](#21-requirements) 1. [Requirements](#21-requirements)
2. [Optional components](#22-optional-components) 2. [Downloading](#22-downloading)
3. [Reporting bugs](#3-reporting-bugs) 3. [Reporting bugs](#3-reporting-bugs)
4. [Running the pipeline](#4-running-the-pipeline) 4. [Running the pipeline](#4-running-the-pipeline)
...@@ -18,8 +18,6 @@ Here, we reproduce the bioinformatics pipeline used by [SPYGEN](http://www.spyge ...@@ -18,8 +18,6 @@ Here, we reproduce the bioinformatics pipeline used by [SPYGEN](http://www.spyge
# 2. Installation # 2. Installation
You will need to install
## 2.1. Requirements ## 2.1. Requirements
In order to run "only_obitools", you need a couple of programs. Most of In order to run "only_obitools", you need a couple of programs. Most of
...@@ -29,10 +27,19 @@ programs and libraries you absolutely need are: ...@@ -29,10 +27,19 @@ programs and libraries you absolutely need are:
- [OBItools](https://pythonhosted.org/OBITools/welcome.html#installing-the-obitools) - [OBItools](https://pythonhosted.org/OBITools/welcome.html#installing-the-obitools)
## 2.2. Optional components ## 2.2. Downloading
Other libraries are optional and only limit the features that are * open a shell
built. These include: * make a folder, name it yourself, I named it workdir
```
mkdir workdir
cd workdir
```
* clone the project and switch to the main folder, it's your working directory
```
git clone http://gitlab.mbb.univ-montp2.fr/edna/nextflow_obitools.git
cd nextflow_obitools
```
# 3. Reporting bugs # 3. Reporting bugs
......
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