megSAP Containerized

This is a containerized version of the Medical Genetics Sequence Analysis Pipeline.

USAGE

1. To run the container interactively (replace YOUR_VOLUME with a path on your host to store the downloads and results):

docker run -i megsap_containerized -m "-v <YOUR VOLUME>:/mnt/data -v <YOUR VOLUME 2>:/tmp"

2. To download the reference genome:

cd megSAP/data/

./download_GRCh37.sh

3. To download databases:

./download_dbs.sh

4. To run somatic_dna pipeline:

cd mnt/data/

php /megSAP/src/Pipelines/somatic_dna.php -p_folder <PATH TO THE FOLDER CONTAINING SAMPLE FOLDERS> -t_id <TUMOUR SAMPLE PROCESSING ID> -n_id <NORMAL SAMPLE PROCESSSING ID> -t_sys <TUMOUR PROCESSING INI FILE> -n_sys <REFERENCE PROCESSING INI FILE> -o_folder <OUTPUT FOLDER>