Workflows in Snakemake for VLPB

In this project, a couple of workflows have been made, the main ones are:

• Genome assembly
• Variant calling
• Genome annotation

To run a workflow, you will need:

• Python 3
• Snakemake
• Biopython

Example

The repository was extracted in /tmp/SnakeMakeVlpb , with git clone https://git.wur.nl/warri004/SnakemakeVLPB.git /tmp/SnakeMakeVlpb.

To let Snakemake find our code, we need to add that directory to the PYTHONPATH:

export PYTHONPATH=$PYTHONPATH:/tmp/SnakeMakeVlpb/

Now we can set everything up:

cd /tmp/SnakeMakeVlpb/src/workflows/assembly/allpaths/noPreprocess

# Install necessary modules in a virtual environment using virtualenv and pip
virtualenv --python=python3 venv
source venv/bin/activate
pip3 install snakemake biopython

Or

# Install necessary modules in a virtual environment using conda and bioconda
conda create --name snakemake python=3 snakemake biopython
source activate snakemake

And then we can simply start the assembly, using the default dataset, as described in config.json:

snakemake

If you want to run a workflow somewhere else, you can tell snakemake to load the workflow from there, but make sure that the PYTHONPATH is set correctly.

cd ~/data ; snakemake --snakefile /tmp/SnakeMakeVlpb/src/workflows/variantCalling/freebayes/Snakefile