The morning will focus on the basics of the Unix shell.
The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks, so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively.
In the afternoon you will put those skills into practice.
You will learn about compute clusters, how to use them for your computations and what are the best practices for it.
Day 2
Second day will focus on using Python in high-performance computing environments to automate data analysis pipelines with Snakemake (for a detailed discussion for why we are teaching Snakemake, see this lesson’s discussion page). We’ll start with the basics and cover everything you need to get started. Some elements of writing performance-oriented code will be covered, but it is not the main focus. There is no prerequisite knowlege for this tutorial, although having some prior experience with the command-line or a compute cluster will be very helpful.
Schedule
Day 1
09:00 - 10:30
Introduction to the Unix shell
10:30 - 10:45
Morning break
10:45 - 12:00
Writing shell scripts
12:00 - 13:00
Lunch break
13:00 - 14:30
Introduction to cluster computing
14:30 - 14:45
Afternoon break
14:45 - 17:00
Hands-on with cluster computing
Day 2
09:00 - 10:30
Introduction to Python basics
10:30 - 10:45
Morning break
10:45 - 12:00
Introduction to Snakemake
12:00 - 13:00
Lunch break
13:00 - 14:30
Writing Snakefiles
14:30 - 14:45
Afternoon break
14:45 - 17:00
Pipeline scaling on a cluster
General Information
Who:
The course is aimed at graduate students and other researchers, particularly from life sciences, who would like to know how a supercomputer can help to accomplish their everyday work.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
Where:
SURF Utrecht. Kantoren Hoog Overborch (Hoog Catharijne), Moreelsepark 48, 3511 EP Utrecht. Room 3.5.
Get directions with
OpenStreetMap
or
Google Maps.
This workshop is sponsored and supported by ELIXIR-EXCELERATE. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.
Setup
You will be granted access to the SURFsara computing facilities during this workshop.
In order to participate, you will need access to the software described below on your laptop,
as well as an up-to-date web browser.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple
tasks more quickly.
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.
Select “Use the nano editor by default” and click on “Next”.
Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.
Click on "Next".
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
Select "Use Windows' default console window" 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]
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of macOS is Bash, 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.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.
Text Editor
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+Q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
Others editors that you can use are
Notepad++ or
Sublime Text.
Be aware that you must
add its installation directory to your system path.
Please ask your instructor to help you do this.
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.
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. 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).
Download the Python 3 installer 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.
Type
bash Anaconda3-
and then press
Tab. The name of the file you just downloaded should
appear. If it does not, navigate to the folder where you
downloaded the file, for example with:
cd Downloads
Then, try again.
Press Return. 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. Type yes and
press enter to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).
