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Setup
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There are several pieces of software you will wish to install before the workshop. Though installation help will be provided at the workshop, we recommend that these tools are installed (or at least downloaded) beforehand.

Python 3

Please install Miniconda. While any installation of Python 3 will work, Miniconda is the free version of Anaconda Python, and comes bundled with its most useful tools. Even better, it includes several significant performance improvements over "vanilla" Python.

Snakemake

Once you have a Miniconda environment configured, please install Snakemake from the bioconda channel with

$ conda install -c bioconda snakemake

{: .language-bash}

Shell and SSH

This lesson requires a terminal application (bash, zsh, or others) with the ability to securely connect to a remote machine (ssh).

Where to type commands: How to open a new shell

The shell is a program that enables us to send commands to the computer and receive output. It is also referred to as the terminal or command line.

Some computers include a default Unix Shell program. The steps below describe some methods for identifying and opening a Unix Shell program if you already have one installed. There are also options for identifying and downloading a Unix Shell program, a Linux/UNIX emulator, or a program to access a Unix Shell on a server.

Shell for Windows

Computers with Windows operating systems do not automatically have a Unix Shell program installed. In this lesson, we encourage you to use an emulator included in Git for Windows, which gives you access to both Bash shell commands and Git. If you have attended a Software Carpentry workshop session, it is likely you have already received instructions on how to install Git for Windows.

Once installed, you can open a terminal by running the program Git Bash from the Windows start menu.

Shell Programs for Windows

Alternatives to Git for Windows

Other solutions are available for running Bash commands on Windows. There is now a Bash shell command-line tool available for Windows 10. Additionally, you can run Bash commands on a remote computer or server that already has a Unix Shell, from your Windows machine. This can usually be done through a Secure Shell (SSH) client. One such client available for free for Windows computers is PuTTY. See the reference below for information on installing and using PuTTY, using the Windows 10 command-line tool, or installing and using a Unix/Linux emulator.

For advanced users, you may choose one of the following alternatives:

Warning

Commands in the Windows Subsystem for Linux (WSL), Powershell, or Cygwin may differ slightly from those shown in the lesson or presented in the workshop. Please ask if you encounter such a mismatch — you're probably not alone. {: .challenge} {: .discussion}

Shell for macOS

On macOS, the default Unix Shell is accessible by running the Terminal program from the /Application/Utilities folder in Finder.

To open Terminal, try one or both of the following:

  • In Finder, select the Go menu, then select Utilities. Locate Terminal in the Utilities folder and open it.
  • Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return.

For an introduction, see How to Use Terminal on a Mac.

Shell for Linux

On most versions of Linux, the default Unix Shell is accessible by running the (Gnome) Terminal or (KDE) Konsole or xterm, which can be found via the applications menu or the search bar.

Special cases

If none of the options above address your circumstances, try an online search for: Unix shell [your operating system].

SSH for Secure Connections

All students should have an SSH client installed. SSH is a tool that allows us to connect to and use a remote computer as our own.

SSH for Windows

Git for Windows comes with SSH preinstalled: you do not have to do anything.

GUI Support for Windows

If you know that the software you will be running on the cluster requires a graphical user interface (a GUI window needs to open for the application to run properly), please install MobaXterm Home Edition. {: .discussion}

SSH for macOS

macOS comes with SSH pre-installed: you do not have to do anything.

GUI Support for macOS

If you know that the software you will be running requires a graphical user interface, please install XQuartz. {: .discussion}

SSH for Linux

Linux comes with SSH and X window support preinstalled: you do not have to do anything.