Commit 40e0be7c authored by peguerin's avatar peguerin
Browse files

Update README.md

parent 0abf102f
......@@ -14,12 +14,10 @@ This was designed to process RADseq data from [RESERVEBENEFIT](https://www.biodi
3. [Set up](#23-set-up)
3. [Reporting bugs](#4-reporting-bugs)
4. [Running the pipeline](#5-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. [Initialisation](#41-initialisation)
2. [Configuration](#42-configuration)
3. [Run the pipeline into a single command](#43-run-the-pipeline-into-a-single-command)
4. [Run the pipeline step by step](#44-run-the-pipeline-step-by-step)
# 1. Introduction
......@@ -131,7 +129,7 @@ verbose as possible — e.g. include the command line, etc
# 4. Running the pipeline
Quickstart
## 4.1 Initialisation
* open a shell
* make a folder, name it yourself, I named it workdir
......@@ -146,9 +144,24 @@ cd workdir
git clone http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2.git
cd snakemake_stacks2
```
## 4.2 Configuration
WORK IN PROGRESS !!!!
## 4.3 Run the pipeline into a single command
One you finished [Initialisation](#41-initialisation)) and [Configuration](#42-configuration) steps. You can run the whole pipeline simply typing :
```
## number of CPU cores available for running the pipeline (for instance here 64 cores)
N_CORES=64
## run the pipeline into a single command
bash main.sh $CORES
```
## 4.4 Run the pipeline step by step
WORK IN PROGRESS !!!!
that's it ! The pipeline is running and crunching your data. Look for the log folder output folder after the pipeline is finished.
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