Pre-requirements¶

What do you need to be prepared?

A good Zoom setup: microphone, camera and a place where you can talk
A shell terminal
- Linux/Bash
- Mac terminal
We recommend VS Code but other coding tools can work
This also includes built-in terminals
Good integrated system
Git/GitHub account and local installation
Python installation

Info

If you have not set up Git/GitHub and have not installed Git, Python and VS code.

Count with ~1 hour of preparations, depending on choices you make (Anaconda takes time to install).

Checkpoints¶

A good Zoom setup¶

You have a Zoom good setup, if:

you can talk freely. If not, find a room/place where you can
others in the Zoom room can clearly hear what you say. If not, use a microphone
you can clearly hear what others in the Zoom room say. If not, use a headset

Visual Studio¶

You have installed Visual Studio, if:

You can start Visual Studio

Do you have Visual Studio Code installed?

Yes!
No, go to Visual studio

Git¶

You have installed git, if:

In a terminal, git version shows your version of git

Don't have Git installed?

Go to Terminal and Git

In a terminal, git config --global user.name shows your name

Does not show your name?

In a terminal, type:

git config --global user.name "[your regular name]"

where [your regular name] is your regular name, for example:

git config --global user.name "Sven Svensson"

In a terminal, git config --global user.email shows your email address

Does not show your email?

In a terminal, type:

git config --global user.email "[your email]"

where [your email] is your email address, for example:

git config --global user.email "sven@svensson.se"

In a terminal, git config --global pull.rebase shows something,

e.g. the text false

Does not show your rebase strategy?

In a terminal, to change this to the default, type:

git config --global pull.rebase false

Can you run Git from VS code?

Yes!
No go to Using git in VS code

Have you configured a Git (local) account?

Yes!
No, go to Configure Git

Have you set up a git ssh-keys?

Test: ssh -T git@github.com
- Output should be something like this: Hi bclaremar! You've successfully authenticated, but GitHub does not provide shell access.
Yes!
If not working, go to to here

You have good enough knowledge of git, if:

You know what cloning is
You know what staging is
You know what a commit is
You know what pushing is
You know what pulling is
You know how to see the status of your git repository
You can do a basic git workflow, as described here in 5 minutes.

Do you know basic git?

I am familiar with basic git commands like
- clone, pull, push, add, commit, status, log
No, go to Git courses

GitHub¶

You have set up a GitHub account, if:

You can login at https://github.com/

Have you set up a GitHub account?

Yes!
No, go to Github

Python¶

You have installed Python, if:

In a terminal, running python --version or python3 --version shows the Python version.

Have you installed Python?

Yes!
No, go to Python

Can you run Python from VS Code?

Yes!
No, go to Python in VS Code

You know enough basic Python, if:

You can describe what a variable is
You can change the value of a variable
You can show the value of a variable on screen

Do you know basic Python?

Yes!
Even though it is not part of the course we will use Python in the exercises.
- With other programming languages you can get far, but you may want to learn the basic syntax used in Python!
To learn more, go to Python courses

Some other solutions¶

Do you want to work in another environment you are used to, you can do some of the steps above and get some inspiration from the other solutions further down.

Visual Studio¶

There are several solutions in how to work with coding and the environments around it

You can work in the environment(s) you are used to.
Many of the teachers will use Visual Studio Code (VS code)
This is not necessary if you have other solution
Benefit:
- integrate you terminal and Git work with code development
- graphical user interface
- available in all platforms
You may want to check VS Code installation as well!
Download
- Note for Mac Users: If Safari does not let you download, try Chrome or other web browser.

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Install Git¶

Git (specific installation may be required) and terminals are already integrated in VS Code and can be the first choice Otherwise follow the steps in the end of this page ([Other solutions]prereqs.md#other-solutions)!

Version >= 2.28 would do

WindowsMacLinux

There are several different ways to run the course material on a Windows computer. Neither is perhaps optimal, and the material itself has not been adapted specifically for Windows. Nevertheless, in principle everything should be possible to run. A few ways you could setup:

Git-windows with a command line and Git integrated

Install Git Windows: https://gitforwindows.org/ (easiest if you want to start fast and plan to work in windows environment)
- Follow the setup insctructions from the Windows part at https://coderefinery.github.io/installation/git-in-terminal/ by CodeRefinery.
- Included will be the Git Bash

We will use terminal to some extent.
Choose one of your choice, the built-in or another!
Chances are big that you already have git installed on your computer.
You can check by running e.g. git --version.
- and if it reports 2.28 or higher, then you are good.
If you have a very old version of git or you don't have it, install it following the instructions here
- You may have to do xcode select --install from the Mac terminal.

git comes installed with all Linux distributions
To install git, do sudo apt-get install git

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Using git in VS code¶

When Git is installed you may need to restart a shell in VS code before it works.

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Configure git¶

This must be done

Follow these instructions. https://nbis-reproducible-research.readthedocs.io/en/course_2104/setup/#installing-git

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GitHub¶

Sign up for GitHub account: https://coderefinery.github.io/installation/github/

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Git–GitHub connection through ssh keys¶

(This may take a while to get working, but is worth it) https://coderefinery.github.io/installation/ssh/

Test: ssh -T git@github.com
Output should be something like this: Hi bclaremar! You've successfully authenticated, but GitHub does not provide shell access.
If not working, these are the approximate steps to be done in your terminal. It can vary between systems, so link above is more certain.

$ ssh-keygen -t ed25519 -C "<email address for your GitHub account>"
$ eval "$(ssh-agent -s)"
$ ssh-add ~/.ssh/id_ed25519
$ # Copy the SSH public key to your clipboard. For WINDOWS:
$ clip < ~/.ssh/id_ed25519.pub

On Mac, use pbcopy instead, like:

$ # Copy the SSH public key to your clipboard. For MAC:
$ pbcopy < ~/.ssh/id_ed25519.pub

Then go to your GitHub account on the web.
1. In the upper-right corner of any page, click your profile photo, then click Settings.
2. In the "Access" section of the sidebar, click SSH and GPG keys.
3. Click New SSH key or Add SSH key.
4. In the "Title" field, add a descriptive label for the new key. For example, if you're using a personal laptop, you might call this key "Personal laptop".
5. Select the type of key authentication.
6. In the "Key" field, paste your public key.
7. Click Add SSH key.
8. If prompted, confirm access to your account on GitHub.
Now test again in your terminal: ssh -T git@github.com
Output should be something like this: Hi bclaremar! You've successfully authenticated, but GitHub does not provide shell access.
If there was a problem, confer the full article Adding a new SSH key to your GitHub account.

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Git courses¶

Learn the basics!
Choose one or several of these!
Git courses
Pro Git book

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Python¶

Use what you already have
If you don't have Python there are different ways to go. We won't use Conda during the lessons, for instance.
- Bare python (recommended for the "bare metal" user)
  - You may need to install other packages (pip)
  - install python
  - note macOS: the system install of Python on macOS is not supported, instead:
    - brew install python3
Anaconda (recommended for python/R developers liking GUI:s) - Count with 15-20 minutes
- includes - many many packages - conda packager - pip installer - GUI launchers, like example - jupyter notebook/lab - Spyder - RStudio - etc... - install Anaconda
- miniconda (recommended for terminal user)
  - Faster to install
  - Includes:
    - less packages than Anaconda, and no GUI launcher but:
    - conda packager
    - pip installer
    - etc...
  - install Miniconda
In Linux and Bash, Python should work from the command line by typing python/python3 or running a script with python <script>/python3 <script>

Python in VS Code¶

Step 1. Install a supported version of Python on your system, see above
Step 2. Install the Python extension for Visual Studio Code from the left menu bar.
Step 3. Open or create a Python file and start coding.
- Example: make a hello.py script and run it with the "play" button.
- Choose which Python interpreter to use.
Step 4. To run Python from a VS Code terminal (Bash or other) you may have to restart the shell

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Python courses¶

We assume familiarity with python at least equivalent
Learn the basics by choosing one or several of these courses!
- Python part of the UPPMAX introductory course
- Python programming with applications to bioinformatics.

Pre-requirements¶

Checkpoints¶

A good Zoom setup¶

Visual Studio¶

Git¶

GitHub¶

Python¶

Some other solutions¶

Visual Studio¶

Install Git¶

Using git in VS code¶

Configure git¶

GitHub¶

Git–GitHub connection through ssh keys¶

Git courses¶

Python¶

Python in VS Code¶

Python courses¶

Other solutions¶

Terminals¶

Python from In Git-bash (Windows)¶