diff --git a/README.md b/README.md index 4e4f944e22a5d80dd9be8b6642cd0c7948bf1a88..13b62853f9ab17ef3506ad7cd33295bb36de4f97 100644 --- a/README.md +++ b/README.md @@ -4,45 +4,4 @@ JASS is a python package that handles the computation of the joint statistics ov ## Documentation -Detailed documentation, describing the setup, usage, and the architecture is available at http://statistical-genetics.pages.pasteur.fr/jass/ - -## install - -You need **python3** to install and use JASS. - -``` -# install -pip install git+https://gitlab.pasteur.fr/statistical-genetics/jass -``` - -## configure and import data - -``` -# configure -export JASS_DATA_DIR=/tmp/JASSDATA -# import GWAS data into JASS -python -m jass create_init_table [TODO use IMpG format] -``` - -## run a server - -``` -# launch celery to process tasks -celery -A jass worker -# launch the web server -python -m jass serve -``` - -## use JASS on the command line - -``` -# 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 -``` - +Detailed documentation, describing the setup, usage, and the architecture is available at http://statistical-genetics.pages.pasteur.fr/jass/ \ No newline at end of file