Commit bdfecba7 authored by Hervé  MENAGER's avatar Hervé MENAGER

remove docs in README which are now in sphinx docs

parent d70947c0
......@@ -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/
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