29905: Introduction to Python for Data Analysis and Automation in Biology

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

1. In the Terminal, type

   cd ~

   and press Enter (or Return depending on your keyboard).
2. Type

   wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

   and press Enter If you get an error message like

   bash: wget: command not found

   , try

   curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

   and press Enter.
3. Type

   bash Miniforge3-$(uname)-$(uname -m).sh

   and then press Enter. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend conda to your PATH (this makes the conda distribution the default Python).
4. Close the terminal window and re-start the Terminal app.
5. Type

   conda config --set auto_activate_base false

   and press Enter to stop conda from auto-activating.
6. Close the terminal window and re-start the Terminal app one more time.
7. Type the following commands, hit Enter after each line:

   conda config --remove channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --set channel_priority strict
   conda activate base
   conda update --yes conda
   conda update --yes --all
     

   Don't worry if the first command results in an error message, we just want to make sure the "defaults" channel is not configured.
8. Lastly, to install Jupyter Lab and all dependencies, type the following commands, hit Enter after each line:

   conda create --yes -n jupyter python=3
   conda activate jupyter
   conda install --yes numpy pandas scikit-learn matplotlib jupyter jupyterlab altair pip git altair odfpy openpyxl seaborn scikit-bio scipy umap-learn wget unzip
       

9. To check your install, type

   wget https://dl.kblin.org/29905/check_install.py

   in your Terminal and hit Enter to download the check script.
10. Then, run

    python3 check_install.py

    . If it prints

    All dependencies installed!

    you're good to go.

1. In the Terminal, type

   cd ~

   and press Enter (or Return depending on your keyboard).
2. Type

   wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

   and press Enter If you get an error message like

   bash: wget: command not found

   , try

   curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

   and press Enter.
3. Type

   bash Miniforge3-$(uname)-$(uname -m).sh

   and then press Enter. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend conda to your PATH (this makes the conda distribution the default Python).
4. Close the terminal window and re-start the Terminal app.
5. Type

   conda config --set auto_activate_base false

   and press Enter to stop conda from auto-activating.
6. Close the terminal window and re-start the Terminal app one more time.
7. Type the following commands, hit Enter after each line:

   conda config --remove channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --set channel_priority strict
   conda activate base
   conda update --yes conda
   conda update --yes --all
     

   Don't worry if the first command results in an error message, we just want to make sure the "defaults" channel is not configured.
8. Lastly, to install Jupyter Lab and all dependencies, type the following commands, hit Enter after each line:

   conda create --yes -n jupyter python=3
   conda activate jupyter
   conda install --yes numpy pandas scikit-learn matplotlib jupyter jupyterlab altair pip git altair odfpy openpyxl seaborn scikit-bio scipy umap-learn wget unzip
       

9. To check your install, type

   wget https://dl.kblin.org/29905/check_install.py

   in your Terminal and hit Enter to download the check script.
10. Then, run

    python3 check_install.py

    . If it prints

    All dependencies installed!

    you're good to go.