Perl minimal version 5.16
Required Bioinformatics tools
There are 3 ways to obtain TOGGLE. We recommend the first one for an install in a cluster.
Create the directory TOGGLE where you want to install TOGGLE and go into this directory
Get the TOGGLE code Clone the git
- Add the Module path to the PERL5LIB environment variable
- In the same way add the TOGGLE directory to the PATH environment variable
Rq : you can add this to the ~/.bashrc to make it always available when you log-in.
- Change the permission of the perl files in the directory TOGGLE
- Modify the file /pathToToggle/modules/localConfig.pm
Modify the shebang of perl in the begining of the script /pathToToggle/toggleGenerator.pl and onTheFly/startBlock.txt
- Test the pipeline with the test data
Modify the path of adaptator file in the file SNPdiscoveryPaired.config.txt
- Check the good running > > * No error message > > * toggleOUTPUT has been created in the /tmp folder > > * the data generated are good
- Test the RNASeq pipeline with the test data
- Check the good running > > * No error message > > * the directory toggleout has been created > > * the directory toggleout/output contain all the results > > * the file toggleout/finalResults/RNASeq.accepted_hits.HTSEQCOUNT.txt has been created > > * the data generated are good
A Docker image based on Ubuntu 14.04 is available at http://bioinfo-web.mpl.ird.fr/toggle/toggle.tgz
If Docker is installed on your system, you can use this image:
You can then download your data in the container (or attach a network/local drive within). TOGGLE can be launch as for a GitHub installation.
This script is dedicated for an installation in the user space (no admin rights required).
Just download it, launch it and follow the instructions.
Then you can launch the different scripts in the TOGGLE folder