BIological Data Analysis Library - Documentation

Requirements

• 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/

netCDF4 output

• sudo apt-get install libnetcdf-dev libhdf5-dev

Installation

Mac OS X

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