Topic outline

  • First Steps with UNIX in Life Sciences

    7 May 2020

    ONLINE

    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact training@sib.swiss.

  • Schedule

    The timing is an approximation and might vary.


    Morning session (9:00 - ~12:30)

    What is UNIX and why should biologists use it?

    UNIX filesystem

    Working with directories and files

    This includes a short "virtual coffee" break.

     

    Afternoon session (~13:30 - 17:00 / 17:30)

    Working with file content

    Working with file content (continued)


    This includes a short "virtual coffee" break.

    • Software install and course material


      REQUIREMENTS:

      You will need to have a command line / terminal program running on your computer, it will be used for the practicals. Depending on your Operating System (OS), it will be more or less simple. Simple for Linux or Mac users.

      Windows users, read below and let us know in advance if you fail installing a terminal program.


      Mac OS X & Linux: a command line program is available by default, but if you have never used it before, locate it (Terminal.app with Mac) and start it. Jump to the last paragraph to read instructions about data download.


      Windows 10: Install a command line program.

      1) Turn ON the "optional features" in the Control Panel. Shortcut: press Windows Key + R to open the Run dialog, type “optionalfeatures”, and press Enter. The list of available Windows features appears. If a feature has a checkmark next to it, it’s enabled. If a feature doesn’t have a checkmark, it’s disabled. Enable the “Windows Subsystem for Linux” option in the list, and then click the “OK” button.



      2) Restart your computer.

      3) In Microsoft Store (you need an account), type Ubuntu (or another one if you know) and install it. After install, open Ubuntu. To get to your usual Documents folder, type cd /mnt/c/Users/yourUsername/Documents.


      Alternatively, instead of installing Ubuntu, you can use the Virtual Machine (VM image) detailed below.


      Older Windows OS: terminal program installation

      We recommend you to install Mobaxterm, which provides all the important remote network tools (SSH, X11, RDP, VNC, FTP, MOSH, ...) and Unix commands (bash, ls, cat, sed, grep, awk, rsync, ...) to Windows desktop, in a single portable exe file which works out of the box. Download link to the free Home Edition: https://mobaxterm.mobatek.net/download.html


      FOR ALL:

      When your terminal is up and running:

      - please download one of the 2 compressed files below (.gz or .zip, easier to uncompress for Windows users) and move the folder to a location you can easily retrieve with the terminal (e.g. avoir folder names with spaces).

      - access the folder "practicals" with the terminal.