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Toolbox for generic NGS analyses

Requirements

Perl minimal version 5.16 ( recommanded 5.20+ )

sudo cpan install Capture::Tiny Data::Translate Data::Dumper Getopt::ArgParse List::Compare Switch Test::More Test::Deep

Integrated Bioinformatics tools

Installing TOGGLe

The following methods are for installing TOGGLe only. The softwares for analyses theselves (e.g. bwa or samtools) must be installed separately.

There are 2 ways to install TOGGLe on a GNU/Linux System in 64bits

  1. From GitHub repository
  2. From the automatic script

From GitHub repository

In the following method, the ‘/path/to/toggle’ represents the absolute path of the installation folder of TOGGLe. You can obtain it by launching a pwd command in this folder.

  • Clone the git repository
git clone https://github.com/SouthGreenPlatform/TOGGLE.git
  • Modify the file /path/to/toggle/modules/localConfig.pm

This file will provide to TOGGLe the paths for all the softwares you will use in your workflows. You can open it using any text editor (e.g. Gedit, nano, mousepad or Leafpad).

Some example of localConfig (based on v0.3.6) are available here for a standard installation.

If your cluster environment supports modules, you can find here examples (v.0.3.6) of toggle toggleModule and of localConfig.pm

If a given tool is not installed, you can leave the line as such. TOGGLe will work only with the tools you request in your workflows.

  • Add the TOGGLe modules path to the PERL5LIB environment variable
export PERL5LIB=$PERL5LIB:/path/to/toggle/modules
  • In the same way add the TOGGLe directory to the PATH environment variable
export PATH=$PATH:/path/to/toggle

Note: you can add this to your ~/.bashrc to make it always available when you log in, as follows:

echo"""
export PERL5LIB=$PERL5LIB:/path/to/toggle/modules
export PATH=$PATH:/path/to/toggle
""" >> ~/.bashrc

From the automatic script

This script is dedicated for an installation in the user space (no admin rights required).

Just download it, launch it and follow the instructions.

$wget https://raw.githubusercontent.com/SouthGreenPlatform/TOGGLE/master/TOGGLEinstall.pl
$perl TOGGLEinstall.pl

Then you can launch the different scripts in the TOGGLe folder