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README.md

STACKS2 using SNAKEMAKE Workflow

RADseq workflow using STACKS2 This was designed to process RADseq data from RESERVEBENEFIT project.

Table of contents

  1. Introduction
  2. Installation
  3. Prerequisite
  4. Data Files
  5. Set up
  6. Reporting bugs
  7. Running the pipeline
  8. Initialisation
  9. Configuration
  10. Run the pipeline into a single command
  11. Run the pipeline step by step

1. Introduction

blablabla

2. Installation

2.1 Prerequisite

You must install the following softwares and packages :

  • SNAKEMAKE 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

    • 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

    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 

    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 :

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/snakemake_stacks2.git
cd snakemake_stacks2

You will see the following folders :

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 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

4.1 Initialisation

  • open a shell
  • make a folder, name it yourself, I named it workdir
mkdir workdir
cd workdir
  • clone the project and switch to the main folder, it's your working directory
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 and 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.