Quick-start

bincs is written as a Snakemake pipeline.

See the installation page for instructions on how to install Snakemake.

The data for this quick-start example can be found at zenodo.

Create the subfolder examples/quick_start/files in the bincs folder and download the dataset.

mkdir bincs/examples/quick_start/files
cd bincs/examples/quick_start/files
wget https://zenodo.org/record/1008923/files/subsample_example_data.tar
tar -xvf subsample_example_data.tar

bincs requires a config file to know what settings to use, and a sample sheet to know what files to use.

They are both in the examples/quick_start/ folder - they are called config.yaml and sample_sheet.txt.

Now, let us invoke Snakemake with the config file given. Go to the main bincs folder and then run Snakemake like so:

cd ../../..
snakemake -pr -j 48 --use-conda --configfile examples/quick_start/config.yaml peaks

This tells Snakemake to run the peaks target with 48 cores. If you have less cores available, just change this parameter.

Running it might take a little while but in the end you should see the output:

localrule peaks:
    input: projects/quick_start/data/peaks/epic/melanocyte.csv,
           projects/quick_start/data/peaks/macs2/melanocyte.csv,
           projects/quick_start/data/peaks/epic/keratinocyte.csv,
           projects/quick_start/data/peaks/macs2/keratinocyte.csv,
           projects/quick_start/data/peaks/epic/fibroblast.csv,
           projects/quick_start/data/peaks/macs2/fibroblast.csv

These are the files created by our invocation of Snakemake.

Let us try one more:

snakemake -pr -j 48 --use-conda --configfile examples/quick_start/config.yaml log2_ratio_heatmaps