Update README.md

5905dce4 · peguerin · b453f3e1 · 5905dce4
Commit 5905dce4 authored Oct 17, 2018 by peguerin
--- a/README.md
+++ b/README.md
-Analyse scripts for map marine genetic diversity
+Analyse scripts for "Global patterns of fish genetic diversity increase with “current” temperature"
 ================================================

-Developed by [Pierre-Edouard Guerin](https://gitlab.com/peguerin)

+Developed by [Pierre-Edouard Guerin](https://gitlab.com/peguerin)
 2017
-
 This folder contains all the scripts to reproduce all the analysis

-## Prerequisite
-You must install the following softwares :
-
-### JULIA Version 0.5.2
-[https://julialang.org/]
-### R Version 3.2.3
-https://cran.r-project.org/
-install.packages("ggplot2")
-install.packages("rgeos")
-please download rgdal at [https://cran.r-project.org/web/packages/rgdal/index.html]
-install.packages("~/Downloads/rgdal_1.1-10.tar.gz")
-install.packages("nodiv")
-install.packages("Cairo")
-### Python Version 2.7.12
-[https://www.python.org/]
-### MUSCLE Version 3.8.31
-[https://www.drive5.com/muscle/downloads.html]
-
-
-## Data Files
+# Table of contents
+
+1. [Introduction](#1-introduction)
+2. [Installation](#2-installation)
+  1. [Prerequisite](#21-prerequisite)
+  2. [Data Files](#22-data-files)
+3. [Scripts Code Source](#3-scripts-code-source)
+
+4. [Reporting bugs](#3-reporting-bugs)
+5. [Running the pipeline](#4-running-the-pipeline)
+  1. [Filter raw data](#51-filter-raw-data)
+  2. [Georeferenced sequences alignments by species](#52-data-files)
+  3. [Species sequence pairwise comparison](#53-species-sequence-pairwise-comparison)
+  4. [Genetic Diversity calculation](#54-genetic-diversity-calculation)
+  5. [Statistical analysis](#55-statistical-analysis)
+
+# 1. Introduction
+
+blablabla
+
+# 2. Installation
+
+
+## 2.1 Prerequisite
+You must install the following softwares and packages :
+
+- [JULIA Version 0.5.2](https://julialang.org/)
+- [R Version 3.2.3](https://cran.r-project.org/)
+    - [R-package]ggplot2 `install.packages("ggplot2")`
+    - [R-package]rgeos `install.packages("rgeos")`
+    - [R-package]rgdal please download rgdal at [https://cran.r-project.org/web/packages/rgdal/index.html] and then `install.packages("~/Downloads/rgdal_1.1-10.tar.gz")`
+    - [R-package]nodiv `install.packages("nodiv")`
+    - [R-package]raster `install.packages("raster")`
+    - [R-package]lme4 `install.packages("lme4")`
+    - [R-package]sp `install.packages("sp")`
+    - [R-package]sjPlot `install.packages("sjPlot")`
+    - [R-package]FactoMineR `install.packages("FactoMineR")`
+    - [R-package]factoextra `install.packages("factoextra")`
+    - [R-package]spdep `install.packages("spdep")`
+    - [R-package]countrycode `install.packages("countrycode")`
+- [Python Version 2.7.12](https://www.python.org/)
+- [MUSCLE Version 3.8.31](https://www.drive5.com/muscle/downloads.html)
+
+## 2.2 Data Files
 The included data files are :

 * `02-raw_data/seqbold_data.txt`                            : Georeferenced sequences of individuals from the supergroup "actinopterygii" have been downloaded from [http://www.boldsystems.org/index.php/Public_SearchTerms?taxon=&searchMenu=records&query=actinopterygii]
-* `01-infos/grid_equalarea200km`                             : Shapefile of worldmap equal area projection epsg:4326 with nested equal area grids (cell sizes of 200km)
+* `01-infos/grid_equalarea200km`                            : Shapefile of worldmap equal area projection epsg:4326 with nested equal area grids (cell sizes of 200km)
 * `01-infos/ne_110m_land`                                   : Shapefile of worldcoast from [http://www.naturalearthdata.com]
 * `01-infos/equalarea_id_coords.tsv`                        : ID and left/right/top/bottom coordinates of each equal area into the shapefile grid_equalarea200km.
 * `01-infos/marine_actinopterygii_species.txt`              : List of "actinopterygii" saltwater species according to [http://www.fishbase.org/]
 * `01-infos/freshwater_behrman_worldcoast_data_object.RData`: R spatial object from "sp package" which is an equal area grid in Berhmann projection with worldcoast shape and presence/absence of freshwater fish species from [https://www.iucn.org/]
 * `01-infos/marine_behrman_worldcoast_data_object.RData`    : ... of marine fish species.
+* IL EN MANQUE...

+# 3. Scripts Code Source
+## 3.1 00-scripts/step1 : filter raw data

-## Scripts code sources
-### 00-scripts/step1 : filter raw data
-======================================
-
-#### BASH scripts
+### 3.1.1 BASH scripts
 * `filter_raw_data.sh`       : Keep only the CO1 sequences with lat/lon information
 * `get_geo_coordinates.sh`   : Uses [http://www.geonames.org/] to find missing coordinates of individual sequences from their textual information of location.

-#### PYTHON scripts
+### 3.1.2 PYTHON scripts
 * `lat_long_DMS_DD_converter.py`     : Converts from DMS format to DD format the given coordinates.

-### 00-scripts/step2 : georeferenced sequences alignments by species
-====================================================================
+## 3.2 00-scripts/step2 : georeferenced sequences alignments by species

 #### BASH scripts
 * `seq_alnt_filtered_data.sh`       : aligns sequences from the same species with MUSCLE and creates coordinates file for each sequence.
@@ -90,32 +111,39 @@ The included data files are :
 * `model_area_GDval.R`
 * `model_species-area_GDval.R`

-## Instructions
-### step1 : filter raw data
-===========================
-bash ./00-scripts/step1/filter_raw_data.sh
-
-### step2 : georeferenced sequences alignments by species
-=========================================================
-bash ./00-scripts/step2/seq_alnt_filtered_data.sh 
-mkdir ./06-species_alnt_cluster/total
-mkdir ./06-species_alnt_cluster/freshwater
-mkdir ./06-species_alnt_cluster/marine
-bash ./00-scripts/step2/cluster_freshwater_vs_marine.sh 
-Rscript ./00-scripts/step2/equalareacoords.R
-
-### step3 : species sequence pairwise comparison
-================================================
-julia ./00-scripts/step3/master_matrices.jl
-
-### step4 : Genetic Diversity calculation
-=========================================
-julia ./00-scripts/step4/equalarea_numbers.jl
-bash ./00-scripts/step4/gdval_by_site.sh
-julia ./00-scripts/step4/metrics_by_area_and_species.jl
-
-### step5 : Statistical analysis
-================================
-Rscript ./00-scripts/step5/model_area_GDval.R
-Rscript ./00-scripts/step5/model_species-area_GDval.R
+
+# 4. Reporting bugs
+
+If you're sure you've found a bug — e.g. if one of my programs crashes
+with an obscur error message, or if the resulting file is missing part
+of the original data, then by all means submit a bug report.
+
+I use [GitLab's issue system](https://gitlab.com/reservebenefit/worldmap_fish_genetic_diversity/issues)
+as my bug database. You can submit your bug reports there. Please be as
+verbose as possible — e.g. include the command line, etc
+
+# 5. Running the pipeline
+
+## 5.1 Filter raw data
+`bash ./00-scripts/step1/filter_raw_data.sh`
+
+## 5.2 Georeferenced sequences alignments by species
+`bash ./00-scripts/step2/seq_alnt_filtered_data.sh `
+`mkdir ./06-species_alnt_cluster/total`
+`mkdir ./06-species_alnt_cluster/freshwater`
+`mkdir ./06-species_alnt_cluster/marine`
+`bash ./00-scripts/step2/cluster_freshwater_vs_marine.sh`
+`Rscript ./00-scripts/step2/equalareacoords.R`
+
+## 5.3 Species sequence pairwise comparison
+`julia ./00-scripts/step3/master_matrices.jl`
+
+## 5.4 Genetic Diversity calculation
+`julia ./00-scripts/step4/equalarea_numbers.jl`
+`bash ./00-scripts/step4/gdval_by_site.sh`
+`julia ./00-scripts/step4/metrics_by_area_and_species.jl`
+
+## 5.5 Statistical analysis
+`Rscript ./00-scripts/step5/model_area_GDval.R`
+`Rscript ./00-scripts/step5/model_species-area_GDval.R`