Python environment setup guide

1. Installing Anaconda2

  1. Download Anaconda2

$ wget https://repo.anaconda.com/archive/Anaconda2-5.1.0-Linux-x86_64.sh

  1. Run the installer (Installer requires bzip, please install it if you don’t have it)

$ bash ./Anaconda2-5.1.0-Linux-x86_64.sh

More information about Anaconda can be found from Anaconda Documentation.

  1. Add Anaconda2 to PATH

$ export PATH=/home/<user>/anaconda2/bin:$PATH
$ . /home/<user>/anaconda2/etc/profile.d/conda.sh

2. Setting up gemx environment to include all conda packages used by GEMX Python APIs.

$ conda config --add channels anaconda
$ conda create --name gemx python=2.7.14 numpy=1.14.5 scipy=1.2.1 -c defaults
$ conda activate gemx
$ conda install pandas=0.24.1
$ conda install keras=2.2.4
$ conda install scikit-learn=0.20.2

Note: above three installation steps are only needed when you first activate the gemx environment.

3. Deactivate gemx environment after testing

Note: Please don’t take this step if you intend to test/use GEMX Python APIs. You only take it after you’ve finished all testing.

$ conda deactivate