- Install python3 from https://www.python.org/downloads/ (version 3.6.2)
- Install git from https://git-scm.com/downloads
- https://virtualenvwrapper.readthedocs.io/en/latest/
- sudo apt-get install libnetcdf-dev libhdf5-dev
Open Terminal
and copy paste below line by line:
mkdir -p ~/{repos,LSData/cache} && cd ~/repos
git clone https://github.com/dicaso/bidali.git
BIDADIR=~/repos/bidali
mkvirtualenv -a $BIDADIR -i ipython -i rpy2 -i twine -i Sphinx \
-r $BIDADIR/requirements.txt bidali
python setup.py test # runs all the tests
deactivate
The bidali package can now be used. The following example illustrates preparing the neuroblastoma 39 cell line data ready for use in R:
. ~/repos/bidali/velsp/bin/activate
python -m LSD --list LSD.dealer.celllines.get_NB39
To update the package, and get new available datasets:
cd ~/repos/bidali git pull origin master . velsp/bin/activate