For this step of the analysis, start a fairly large instance if running from scratch, say about an r2.8xlarge (8 cpus with 61 GB RAM). After your Notebook Session has initilased in CloudOS, open a terminal type the following command:
Postpone opening an .ipynb file until you have completed all teh following steps, to make sure your Notebook environment is the updated one, after the installations have been successfully completed.
git clone https://github.com/TheJacksonLaboratory/sbas.gitFollow the instructions to configure the git config, your GitHub associated email and name.
cd sbas
Open a terminal and type the following command:
conda init
This will prepare your environment to be able to use conda. After the command has been executed, close this terminal and open a fresh one.
You might be prompted to do so by conda as well.
cd sbas
conda env update --name base --file dependencies/requirements.txt
conda activate base
Along with some other dependencies:
cd sbas
Rscript dependencies/install.R
Your environment is ready now, you can open your .ipynb file and start working on your Jupyter Notebook.