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Commit 5bbb4c97 authored by peguerin's avatar peguerin
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Merge branch 'master' of http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2

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README.md
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......@@ -12,14 +12,12 @@ This was designed to process RADseq data from [RESERVEBENEFIT](https://www.biodi
1. [Prerequisite](#21-prerequisite)
2. [Data Files](#22-data-files)
3. [Set up](#23-set-up)
3. [Reporting bugs](#4-reporting-bugs)
3. [Reporting bugs](#3-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
......@@ -34,64 +32,70 @@ blablabla
You must install the following softwares and packages :
- [SNAKEMAKE 5.3.0](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html)
Check version and if the program is correctly installed by typing :
```
snakemake --version
## should give you the output
5.3.0
```
* Check version and if the program is correctly installed by typing :
```
snakemake --version
## should give you the output
5.3.0
```
- [STACKS 2.0b](http://catchenlab.life.illinois.edu/stacks/)
Check version and if programs are correctly installed by typing :
```
process_radtags --version
clone_filter --version
gstacks --version
populations --version
## should give you the output
2.0b
```
* Check version and if programs are correctly installed by typing :
```
process_radtags --version
clone_filter --version
gstacks --version
populations --version
## should give you the output
2.0b
```
- [BWA 0.7.17](https://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial)
Download `bwa` at: http://sourceforge.net/projects/bio-bwa/files/
```
tar -xvf bwa-x.x.x.tar.bz2
cd bwa-x.x.x
./configure --prefix=/where/to/install
make
make install
```
Check version and if programs are correctly installed by typing :
```
bwa
## should give you the output
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
...
```
- [SAMTOOLS](http://www.htslib.org/)
Download `htslib` and `samtools` at : http://www.htslib.org/download/
Building each desired package from source is very simple:
```
cd htslib-1.x
./configure --prefix=/where/to/install
make
make install
cd ..
## and similarly for samtools :
cd samtools-1.x
./configure --prefix=/where/to/install
make
make install
```
Check version and if programs are correctly installed by typing :
```
samtools --version
## should give you the output
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.
```
* Download `bwa` at: http://sourceforge.net/projects/bio-bwa/files/
```
tar -xvf bwa-x.x.x.tar.bz2
cd bwa-x.x.x
./configure --prefix=/where/to/install
make
make install
```
* Check version and if programs are correctly installed by typing :
```
bwa
## should give you the output
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
...
```
- [SAMTOOLS 1.9 ](http://www.htslib.org/)
* Download `htslib` and `samtools` at : http://www.htslib.org/download/
* Building each desired package from source is very simple:
```
cd htslib-1.x
./configure --prefix=/where/to/install
make
make install
cd ..
## and similarly for samtools :
cd samtools-1.x
./configure --prefix=/where/to/install
make
make install
```
* Check version and if programs are correctly installed by typing :
```
samtools --version
## should give you the output
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.
```
## 2.2 Data Files
The included data files are :
......@@ -105,24 +109,27 @@ The included data files are :
clone the project and switch to the main folder, it's your working directory
```
git clone dzdzdzworldmap_fish_genetic_diversity.git
git clone http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2.git
cd snakemake_stacks2
```
You will see the following folders :
# 4. Reporting bugs
# 3. 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)
I use [GitLab's issue system](https://gitlab.com/reservebenefit/snakemake_stacks2/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
# 4. Running the pipeline
Quickstart
## 4.1 Initialisation
* open a shell
* make a folder, name it yourself, I named it workdir
......@@ -134,10 +141,27 @@ cd workdir
* clone the project and switch to the main folder, it's your working directory
```
git clone
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
Once 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 $N_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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