Cluster Computing for Life Sciences

Jul 1-2, 2019

9:00 am - 17:00 pm

Instructors: Carlos Teijeiro Barjas (SURFsara)

Helpers: (to be confirmed)

Syllabus

Day 1

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.

When: Jul 1-2, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.).

Contact: Please email mateusz.kuzak@dtls.nl or carlos.teijeiro@surfsara.nl for more information.


Sponsors

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.

EXCELERATE

Surveys

Please be sure to complete following survey after the workshop.

Post-workshop Survey


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.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. 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.
    2. Select “Use the nano editor by default” and click on “Next”.
    3. 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.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Select "Use Windows' default console window" and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. 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.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

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. 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).

  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. 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.)
  3. Open a terminal window.
  4. 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.
  5. 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).
  6. Close the terminal window.

Downloading sample files for Day 1

Please execute the following commands in the terminal to download the sample files for the 1st day:

curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/004/SRR2589044/SRR2589044_1.fastq.gz ; gunzip SRR2589044_1.fastq.gz

curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/004/SRR2589044/SRR2589044_2.fastq.gz ; gunzip SRR2589044_2.fastq.gz

curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_1.fastq.gz ; gunzip SRR2584863_1.fastq.gz

curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_2.fastq.gz ; gunzip SRR2584863_2.fastq.gz

curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/006/SRR2584866/SRR2584866_1.fastq.gz ; gunzip SRR2584866_1.fastq.gz

curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/006/SRR2584866/SRR2584866_2.fastq.gz ; gunzip SRR2584866_2.fastq.gz