Commit 12c33954 authored by peguerin's avatar peguerin
Browse files

readme update

parent f30e47a5
......@@ -10,9 +10,10 @@ Submited to Nature communications, 2019
1. [Introduction](#1-introduction)
2. [Installation](#2-installation)
1. [Prerequisites](#21-prerequisites)
2. [Data Files](#22-data-files)
3. [Set up](#23-set-up)
1. [Prerequisites](#21-prerequisites)
2. [Singularity container](#22-singularity-container)
3. [Data Files](#23-data-files)
4. [Set up](#24-set-up)
3. [Scripts Code Source](#3-scripts-code-source)
4. [Running the pipeline](#4-running-the-pipeline)
1. [Filter raw data](#41-filter-raw-data)
......@@ -27,6 +28,7 @@ Submited to Nature communications, 2019
6. [Taxonomy and habitat attributed to each individual sequences](#46-taxonomy-and-habitat-attributed-to-each-individual-sequences)
# 1. Introduction
This repository contains all the scripts to reproduce the results of the paper Manel et al. (2019) from the georeferenced barcode sequences of the supergroup "actinopterygii" downloaded from [BOLD](http://www.boldsystems.org/index.php/Public_SearchTerms?taxon=&searchMenu=records&query=actinopterygii) on 17th september 2018.
......@@ -90,7 +92,31 @@ For [Figures and statiscal analysis](#45-statistical-analysis), only R packages
- `python3-module` difflib
- [MUSCLE Version 3.8.31](https://www.drive5.com/muscle/)
## 2.2 Data files
## 2.2 Singularity container
Alternatively, you can download and use a singularity container with all prerequisites (R, Julia, Python, Muscle).
### Install Singularity
See https://www.sylabs.io/docs/ for instructions to install Singularity.
### Download the container
```
singularity pull --name global_fish_genetic_diversity.simg shub://Grelot/global_fish_genetic_diversity:global_fish_genetic_diversity
```
### Use the container
This command will spawn a shell environment with all prerequisites.
```
singularity shell global_fish_genetic_diversity.simg
```
## 2.3 Data files
The included data files are :
* [seqbold_data.tsv](02-raw_data/seqbold_data.tsv) : georeferenced barcode sequences of the supergroup "actinopterygii" downloaded from [BOLD](http://www.boldsystems.org/index.php/Public_SearchTerms?taxon=&searchMenu=records&query=actinopterygii) on 17th september 2018
......@@ -112,7 +138,7 @@ The included data files are :
* [distanceCote](01-infos/distanceCote.csv) : distance from shore for each cell calculated from [gmed](http://gmed.auckland.ac.nz/)
* _ornament_ [fishes images](01-infos/images) :free silhouette images of fishes from [phylopic](http://phylopic.org/)
## 2.3 Set Up
## 2.4 Set Up
Clone the project and switch to the main folder, it's your working directory
```
......
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