run_poppunk

Run poppunk in python

1. Download input data and code

git clone git@github.com:muppi1993/run_poppunk.git

2. Download and unpack database

cd run_poppunk
wget https://sketchdb.blob.core.windows.net/public-dbs/GPS_v4_full.tar.bz2
tar -xf GPS_v4_full.tar.bz2

If you already have the database saved on your machine, you can also adjust db_path in try_poppunk.py at line 24 to the location of the database on your machine.

3. Install PopPUNK

conda install poppunk

If you can't use conda yet, you can get Miniconda to use it. If you can't find the package, you might need to run this first:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

4. Run popppunk

python3 try_poppunk.py