Spike

Spike is one of SNuPy's brothers.

NGS pipeline for SNV detection in tumor context

Install

1. make sure you have installed Miniconda: https://conda.io/miniconda.html
2. clone this repo into suitable location.
3. install snakemake conda install -c bioconda -c conda-forge snakemake - if within UKD network, you might have to force conda to not use certificates conda config --set ssl_verify false
4. install seaborn: conda install seaborn try this command if the above one dose not work conda install -c conda-forge seaborn 5. install beautifulsoup4: conda install beautifulsoup4 -c anaconda
5. new depencencies: biom-format and h5py for conversion to biom to finally compute sample distances: conda install -c bioconda -c anaconda biom-format h5py xlsxwriter xlrd -y try this command if the above one dose not work conda install -c conda-forge -c bioconda -c anaconda biom-format h5py xlsxwriter xlrd -y