FIXME docker
Setup
To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
- Download the Git for Windows installer.
- Run the installer and follow the steps below:
- Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
- From the dropdown menu select "Use the nano editor by default" and click on "Next".
- Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
- Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
- Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
- Ensure that "Use Windows' default console window" is selected and click on "Next".
- Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
- Click on "Install".
- Click on "Finish".
-
If your "HOME" environment variable is not set (or you don't know what this is):
- Open command prompt (Open Start Menu then type
cmd
and press [Enter]) -
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
- Press [Enter], you should see
SUCCESS: Specified value was saved.
- Quit command prompt by typing
exit
then pressing [Enter]
- Open command prompt (Open Start Menu then type
This will provide you with both Git and Bash in the Git Bash program.
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 enter/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".
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/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
.
Docker
Docker Compose relies on Docker Engine for any meaningful work, so make sure you have Docker Engine installed either locally or remote, depending on your setup.
We use Chocolatey to install Docker. See the pipx installation section to install Chocolatey.
Use docker-desktop for an easier installation if you have Windows Pro or Enterprise and a DockerHub account:
choco install docker-desktop
If you have Windows home or don't want to create a DockerHub account, use docker-toolbox:
choco install docker-toolbox -ia /COMPONENTS="kitematic,virtualbox,dockercompose" -ia /TASKS="desktopicon,modifypath,upgradevm"
Open the Docker Quickstart Terminal to start Docker.
Additional components that might be needed to install (VM and GUI):
choco install virtualbox docker-kitematic
Virtualization and Hyper-V must be
activated. Check in the Task Manager,
in tab Performance
if Virtualization is enabled.
Check the documentation to enable it.
- Docker-desktop installation will propose to install virtualization automatically after the Docker installation, if they are not installed.
- Note that Docker Hyper-V is not available for Windows 10 Home edition (you will need Pro or Enterprise edition)
- You might need to access the BIOS to enable VT-x virtualization
- Share drive
By default docker-desktop
and docker-toolbox
are sharing your C:/Users
volume. Docker will only be able to access folders and files in the Shared Drives.
So make sure you execute d2s init
somewhere in your users directories.
On docker-desktop
you can change it in Docker config > Settings
> Shared Drives
> Share Drive C
On docker-toolbox
you need to change the settings of the Virtual Box
Use the
Docker installer for MacOS ( .dmg
file) to install Docker and docker-compose.
If you have a DockerHub account you can use the DockerHub installer instead.
You can change Docker settings by clicking on the Docker icon 🐳 in the top bar, then click Preferences...
The volumes /Users
and /tmp
should be shared by default. It is recommended to create the d2s
project folder in a subfolder of /Users.
Install Docker and docker-compose.
sudo apt update
sudo apt install docker.io
sudo systemctl enable --now docker
sudo usermod -aG docker ${USER}
# Install docker-compose
sudo curl -L "https://github.com/docker/compose/releases/download/1.24.1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
sudo chmod +x /usr/local/bin/docker-compose
sudo groupadd docker
could be required before usermod
if the group has not been created.
Git
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your /Applications
folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git
and for Fedora run
sudo dnf install git
.
Python
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).
We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).
- Open https://www.anaconda.com/distribution/#download-section with your web browser.
- Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
- Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
- Open https://www.anaconda.com/distribution/#download-section with your web browser.
- Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
- Install Python 3 by running the Anaconda Installer using all of the defaults for installation.
- Open https://www.anaconda.com/distribution/#download-section with your web browser.
- Download the Anaconda Installer with Python 3 for Linux.
(The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.) - Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
-
Type
bash Anaconda3-
and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear. -
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 to approve the default location for the files. Typeyes
and press Enter to prepend Anaconda to yourPATH
(this makes the Anaconda distribution the default Python). - Close the terminal window.