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This repository contains scripts, called handlers, that automate the process of converting raw FASTQ sequences into BAM files, and finally to a finished VCF file.
To set up RNApipeline, open a terminal and type:
git clone https://github.com/LappalainenLab/RNApipeline.gitIf you don't have Git installed, you can go to the repository on GitHub and select Download ZIP on the right-hand side. No GitHub account is required for downloading through either method.
To see usage information about RNApipeline, go into the sequence handling directory
cd RNApipelineand run:
./main.shThis repository has a heavy dependency on GNU Parallel; most of the handlers use GNU Parallel to speed the processing of multiple samples. While this speeds processing, be aware that: standard laptops, tablets, and desktop computers may not be appropriate. The handlers in the repository are most appropriate for use on supercomputers; this pipeline was designed for compute clusters oriented around the Grid Engine.
MSI's resources make extensive use of a module system, in which software is installed and maintained by MSI and users can call upon modules as needed. These handlers are designed to call upon modules whenever possible, however some dependencies are only available through the Morrell Lab. To gain access to the Morrell Lab modules, please run the following command on the login host:
echo export MODULEPATH=/panfs/roc/groups/9/morrellp/public/Modules:'$MODULEPATH' >> ~/.bash_profilePlease check the dependencies page to see which programs are necessary for each handler.
Before beginning RNApipeline, make sure that your FastQ samples have been merged (if individual samples are split across multiple files) and renamed. It will be much harder to merge and/or rename files later in the pipeline.
- Install or locate the correct version of each of the dependencies
- Create a list of your samples
- Fill out a configuration file for your project