---
tags: BMMB554-23
---

# Lecture 3: Shell II

[](https://xkcd.com/354)

Shell allows interaction with operating system. Today we will play with [bash](https://en.wikipedia.org/wiki/Bash_(Unix_shell)), which is one of [many](https://en.wikipedia.org/wiki/Comparison_of_command_shells#General_characteristics) existing shells.

## Lecture setup

1. Start [JupyterLab](https://mybinder.org/v2/gh/jupyterlab/jupyterlab-demo/try.jupyter.org?urlpath=lab)
2. Start terminal within JupyterLab instance


3. Download notebook for today's lecture into the JupyterLab environment by executing the following command (cut the command and paste it into terminal you opened at step 2)

wget https://raw.githubusercontent.com/nekrut/BMMB554/master/2023/ipynb/L3-shell2_ws.ipynb

4. Refresh your file browser
5. Double click on the notebook to launch it (select Python 3 kernel)
6. Drag notebook tag to a side to have side-by-side view of the notebook and terminal.
7. Go to terminal tab end execute the following commands:

cd ~/
mkdir -p Desktop/
cd Desktop/
wget -c https://github.com/swcarpentry/shell-novice/raw/2929ba2cbb1bcb5ff0d1b4100c6e58b96e155fd1/data/shell-lesson-data.zip
unzip -u shell-lesson-data.zip

8. Let the lecture begin!

## A note on UNIX shortcuts

{%gist tuxfight3r/60051ac67c5f0445efee %}

## A note on package managers (and virtual environments)


Today we will use a package manager called [`Conda`](https://docs.conda.io/en/latest/). It is used to install software and to manage *virtual environments* (more about virtual environments when we talk about Python programming). Today we will use `Conda` to install a directory structure visualizer[`tree`](https://en.wikipedia.org/wiki/Tree_(command)):

conda install tree

to make things faster you can also use an alternative implementation of`Conda`called[`mamba`](https://mamba.readthedocs.io/en/latest/):

mamba install tree

## Quiz 1

> (You will receive instructions at the end of the lecture)