GenEpi-BioTrain - Virtual training 09 & 10 - Unix for beginners & Introduction to the Conda ecosystem

Topic outline

• Virtual training 09 & 10: Unix for beginners & Introduction to the Conda ecosystem

  Virtual training 09 & 10: Unix for beginners & Introduction to the Conda ecosystem

  ℹ️ Please Note

  You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 09 & 10 held in August 2024, and certificates are only issued to participants who attended the live webinar sessions.

  Introduction
  

  Welcome to the virtual training on "Unix for beginners & Introduction to the Conda ecosystem"!

  This course aims at providing you with a general introduction to working in Unix as well as to creating Conda environments for running simple bioinformatics tasks.
  

  This training is VERY light on bioinformatics content and is mainly aimed at navigating Unix and understanding Conda. If you already have experience of working with Unix terminals and have tried to set up your first environment, this course may not be for you.
  

  On the other hand, if you need to do bioinformatics analysis on your own account, but haven't had the opportunity or time to get properly acquainted with Unix, this may be your chance to get started.
  

  
  

  Get you started in bioinformatics
  

  If you are a beginner in bioinformatics, this course is recommended as the very first course to take, before looking at all the other GenEpi-BioTrain Virtual Trainings and at the learning material of the "Bridging the Gaps in Bioinformatics" course.

  
  

  IMPORTANT! Prerequisites

  The main assumption of this course is that in order to work with bioinformatics, you need to work in a Unix ecosystem. Therefore, to get the most out of this course and any future bioinformatics work, you should consider using a Unix-based operating system (either MacOS or any Linux distribution). If you don't have access to such a system, please follow the "Ubuntu installation instructions" below, which is a thorough guide to installing Ubuntu on a PC (even very old PCs can be used, and this guide has been tested on a complete beginner!).

  Note that the course material and demonstration will be performed from a laptop with Ubuntu preinstalled.

  
  

  Micromamba

  In the third and final session, you will work with Micromamba to install and run bioinformatic software. At the time of writing the official documentation on installation requires the use of the command-line program "curl", in order to install this, execute the following command in an terminal window in Ubuntu:

  sudo apt-get install curl  # Provide you password to proceed with the installation

  For the best possible outcome ensure to read up on the installation instructions for you operating system on the Micromamba installation page.
  https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html
  
  For Ubuntu that commands is (as of wirtting):
  

  "${SHELL}" <(curl -L micro.mamba.pm/install.sh)

  
  For MacOS it is:
  

  brew install micromamba

  
  

  For MacOS users

  The course material are made from the base assumption of installing Micromamba from Ubuntu. As installation of Micromamba on MacOS requires the use of the `Brew` system, participants are required to make themselves acquinted with setting up and using `Brew` for installing Micromamba. An (untested) guide to set up Brew for MacOS can be found here:
  https://www.cyberciti.biz/faq/how-to-install-homebrew-on-macos-package-manager/
  

  
  

  Teams in Ubutnu

  Once installation of Ubuntu is finished, Teams can be easily installed, enabling you to follow along the course and exercises from the same laptop. Boot into Ubuntu, click in the top left corner icon of the navigation bar (Shows a thin white bar and a small grey dot). Type "App center" in the search bar and open the program of the same name.

  In the App center search "teams-for-linux" and click on the app of the same name. Press install.

  Teams are now available to open when clicking the top left icon (search for "teams")
  

  
  

  Sessions

  The three sessions take place on 20, 21 and 22 August at 10:00-14:00 (CET) on each day.
  

  As with all GenEpi-BioTrain Virtual Trainings, the webinars will be recorded and you will be able to access the recordings at any time, provided you are enrolled in the course.

  • PageUbuntu installation instructions
  • FileUbuntu Installation instructions - PDF
  • ForumAnnouncements
  • PageLegal terms and conditions
• Session 1 (20 August) - Basic Navigation in Unix

  Session 1 (20 August) - Basic Navigation in Unix

  The aim of the first session is to introduce the participants to the Unix ecosystem. Emphasis will be placed on understanding the hierarchical file system that Unix is structured around to ensure that the participants can more easily navigate the system. At the same time, the participants will be introduced to basic Unix commands which can be useful for inspecting various files.
  

  After attending this session, participants will be able to:

  • Understand and recognize Unix as an ecosystem
  • Execute several basic commands in the terminal
  • Navigate in Unix

  • PageAgenda - Day 1
  • FolderResources
  • H5PSession 1 recording
  • 
    

• Session 2 (21 August) - Advanced Exploration in Unix

  Session 2 (21 August) - Advanced Exploration in Unix
  The aim of the second session is to expand the knowledge of basic Unix commands. The participants will work with file manipulation and consolidate their understanding of the power of the command line interface.

  
  

  After attending this session, the participants will be able to:

  • Run simple commands for inspecting files
  • Manipulate file contents from command line
  • Learn how to execute a file as a command, in contrast to pointing to its location
    

  • PageAgenda - Day 2
  • FolderResources
  • H5PSession 2 recording
  • 
    

• Session 3 (22 August) - The "Conda ecosystem" for Bioinformatics tasks

  Session 3 (22 August) - The "Conda ecosystem" for Bioinformatics tasks

  This third session aims to enhance participants’ ability to perform bioinformatics tasks in the command line, through setting up and evoking environments. The participants will be introduced to package management systems and will be able to explain the advantages of setting up separate environments with bioinformatic tools.

  In this context, they will be introduced to the use of the Anaconda platform (Reffered to as Conda in daily talk) for setting up environments and managing software packages within these environments. Participants will be given a demonstration of the installation of an Anaconda-package manager called Micromamba, and then set up their own environments with software packages. Finally, participants will evoke their own environments and run a simple bioinformatic tool on a handful of publicly available WGS data of bacterial isolates.

  After attending this session, the participants will be able to:

  • Understand principles behind package management in separate environments
  • Have a basic understanding of the Conda ecosystem for handling environments and packages
  • Download and install Micromamba on Ubuntu
  • Use Micromamba - A Conda ecosystem package manager
  • Create and activate environments
  • Install several bioinformatics software
  • Run a bioinformatics analysis

  • FolderConda resources
  • H5PSession 3 recording
  • 
    

• Contacts

  Contacts

  For any questions regarding the this webinar series, please use the discussion forum.

  If you have questions regarding other training initiatives please contact: courses@ecdc.europa.eu.

  If you have technical issues please contact ECDC Helpdesk - ICT Front Office ICT.FrontOffice@ecdc.europa.eu.