mpn-aml-pairtree

Source code used in combination with Pairtree for studying the cancer evolution from myeloproliferative neoplasm (MPN) to acute myeloid leukemia (AML).

Requirements

Python 3+

Installation

Clone repository

git clone https://github.com/ethanumn/mpn-aml-pairtree.git && cd mpn-aml-pairtree

Setup virtual environment

virtualenv env
echo "" >> env/bin/activate
echo "# Environment Variables" >> env/bin/activate
echo "export DATA_DIR=$PWD/data" >> env/bin/activate
echo "export UTILS_DIR=$PWD/utils" >> env/bin/activate
source env/bin/activate

Install dependencies

pip3 install -r requirements.txt

Example

To run an example, run the following commands. Then, view the example.ssm and example.params.json, as well as the example input files used.

$UTILS_DIR/pipeline_scripts/example.pipeline && cd $DATA_DIR/example