An introduction to Python for Bioinformatics
To run python, we are going to use Jupyter Notebooks. The easiest way to get started using python is to install Anaconda, with Python 3.7.
Choose the version which matches your operating system. When asked if you want to add Anaconda to the path, choose yes.
If you want to have access to the Anaconda distribution on the HPCC, follow the instructions on this page.
Open a terminal, either using the terminal app in MacOS or by searching "cmd" in the Windows search box.
Use the command ls to show the files and folders in the current directory, then use cd <myfolder> to navigate into your desired location (replacing <myfolder> with the folder name).
Run this command: git clone https://github.com/liberjul/Python_for_Beginners (type or copy+paste the command, press Enter)
If your computer did not recognize the command git, install git using this link.
As new material is uploaded, you will need to run through these commands:
git add <saved_file1> <saved_file2> ...
git commit -M "<my message>"
git pull
Now run this: jupyter lab
Now you can navigate to the Python_for_Beginners directory and run the notebooks in the Exercises directory.
If any package fails to import, you may want to look up the packages install directions. Generally, one of these commands will work when run on the command line (terminal or command prompt):
pip install <packagename>
conda install <packagename>
Click on the notebook links to run them in Google Colab: