Commit bd1db8b5 authored by peguerin's avatar peguerin
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Update README.md

parent 70f0eace
......@@ -9,6 +9,7 @@ This folder contains all the scripts to reproduce all the analysis
2. [Installation](#2-installation)
1. [Prerequisite](#21-prerequisite)
2. [Data Files](#22-data-files)
3. [Set up](#23-set-up)
3. [Scripts Code Source](#3-scripts-code-source)
4. [Reporting bugs](#3-reporting-bugs)
5. [Running the pipeline](#4-running-the-pipeline)
......@@ -57,6 +58,20 @@ The included data files are :
* `01-infos/marine_behrman_worldcoast_data_object.RData` : ... of marine fish species.
* IL EN MANQUE...
## 2.3 Set Up
clone the project and switch to the main folder, it's your working directory
```
git clone http://gitlab.mbb.univ-montp2.fr/reservebenefit/worldmap_fish_genetic_diversity.git
cd worldmap_fish_genetic_diversity
```
Then you will need to download georeferenced sequences of actinopterygii individuals "combined TSV file" from [http://www.boldsystems.org/index.php/Public_SearchTerms?taxon=&searchMenu=records&query=actinopterygii]
Store it into the folder `02-raw_data` and rename it `seqbold_data.txt`
You're ready to run the analysis. Now follow the instructions at [Running the pipeline](#4-running-the-pipeline)
# 3. Scripts Code Source
## 3.1 `00-scripts/step1` : filter raw data
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