sjanssen2 / spike

NGS pipeline for SNV detection in tumor context
BSD 3-Clause "New" or "Revised" License
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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