Instructions

Please see guidelines below to run this code.

Setup conda environment

1. For more information on how to create and activate conda activate see this link https://www.anaconda.com/docs/getting-started/working-with-conda/environments. However, these are the two basic commands for creating and activating conda environments.

    conda create -n <ENV_NAME>
   
    conda activate <ENV_NAME>
   

   NB: Replace <ENV_NAME> with the name of your environment

2. Use which python and which pip to make sure the environment is using the appropriate python

3. Next, download the git repo - ideally in a new folder.

4. Make sure you're in the same directory where the setup.py is located before running the following command:

    pip3 install -e . 
   

   The command above downloads relevant dependencies to run probeSeq module

5. To see which libraries/packages have been download use the following command:

    pip3 list
   

How to run / open juptyer notebook

6. Change your directory to where processGenbank.ipynb is located on your computer, and then use juptyter notebook into your terminal. This will trigger your browser and open the probePanel directory.

7. Click on processGenbank.ipynb to open the notebook.