Make a folder data/user_input/ where you put your count data with filetype .tsv and your metadata with filetype .txt. Change the folders in config/config.yaml with your respective file names. Further change the config file to your liking.
conda create -n [Name of your choice] snakemake=8.10.0
conda install graphviz # For visualisation of the DAG (see below)Activate your conda environment with Snakemake and change the working directory to your directory of choice.
conda activate [Name of your snakemake conda]
cd [Path to working directory]Make sure you open the interface of Cytoscape. Otherwise, this will lead to errors in the rule rule cytoscape_enrichmentmap. This is done with:
Cytoscape/CytoscapeChange the 4 with the amount of cores you would like to use.
snakemake --resources cytoscape_instances=1 --use-conda -c 4--resources cytoscape_instances=1 makes sure to only run one Cytoscape rule at a time, because you can not have multiple Cytoscapes open at a time. --use-conda activates the .yaml conda environments for each rule. -n can be added to perform a dry run, to show the rules which are going to be executed.
Visualisation of the order of the rules in the Snakemake.
snakemake --dag -c 1 | dot -Tsvg > dag.svg
# Use the command below for a simplified DAG
snakemake --rulegraph -c 1 | dot -Tsvg > rulegraph.svg