JASS

# install
pip install [TODO upload to pypi]

# configure
export JASS_DATA_DIR=/tmp/JASSDATA
# import GWAS data into JASS
python -m jass create_init_table [TODO use IMpG format]

# launch celery to process tasks
celery -A jass worker
# launch the web server
python -m jass serve

# list available phenotypes on the command line
python -m jass list-phenotypes
# compute joint statistics on the command line into an HDF file
python -m jass create-worktable --phenotypes z_RA_RA z_ReproGen_AME --worktable-path testwt.h5
# create the global manhattan plot for a joint statistics file
python -m jass plot-manhattan --worktable-path testwt.h5 --plot-path testgm.png
# create the quadrant plot for a joint statistics file
python -m jass plot-quadrant --worktable-path testwt.h5 --plot-path testqd.png