ride_snakemake.md

RiDE

RiDE (RNA Differential Expression) is a pipeline for RNA-seq data analysis.

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Requirements

RiDE pipeline contains the instruction to automatically download and install all required dependecies. The only required software is asked to install is Conda.

Usage

Preliminary Steps

For pipeline manual execution, just clone the git repository:

git clone https://github.com/solida-core/ride

The ride/ folder contains all files required for pipeline execution, apart data-related files that the user have to include in the folder.

As mentioned above, Snakemake will manage all pipeline requirements, but we need to work in a virtual environment in which is installed Snakemake. The instructions are included in the environment.yaml file.

• Create the project virtual environment:

conda env create --name my_environment_name --file environment.yaml

• Activate the project virtual environment:

source activate my_environment_name

Run Snakemake

Now that the virtual environment is created and activated, it is possible to execute the pipeline. Starting from final output indicated in the rule_all section of the Snakefile, Snakemake will check for rules and input required for producing those files. In this way, it is possible to perform a test-check called dryrun:

snakemake --snakefile Snakefile --configfile my_config.yaml --dryrun

The process will display, in absence of errors, all steps that need to be executed to obtain output indicated in the Snakefile's rule_all and the number of each rule execution repeat based on the number of samples.

The built graph can also be plotted with the following command:

snakemake --configfile my_config.yaml --dag | dot -Tpng > my_graph.png

Finally, the execution of the pipeline can be launched with the command:

snakemake --snakefile Snakefile --configfile my_config.yaml

For further Snakemake options type:

snakemake --help