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Installation instructions

TEST TEST TEST

We ask all students to bring their own laptop and to install the required software before the beginning of the practicals. We will provide a troubleshooting session on Tuesday (19.9.2023), after the lecture, for those who need to resolve installation issues.

For the course, we will be using the following software:

  1. Docker
  2. QIIME2
  3. FastQC

Please follow the instructions provided according to the operating system (OS) you are using. Feel free to email us with questions if you encounter installations issues bioinformatics.bme307@gmail.com. See you soon!

For Windows Users:

1. Docker + QIIME2

Is "Virtualization" enabled?

  • Press Ctrl + Alt + Del
  • Select Task Manager
  • Click the Performance tab
  • Click CPU
  • Is "Virtualization:" enabled?
  • If not, you can follow the instructions on how to enable virtualization in BIOS here.

The instructions may vary depending on the laptop you are using. The link includes instructions for Acer, Assus, Dell, HP, Lenovo, Sony, and Toshiba.

  • Install Docker Desktop on Windows from here
  • Run the .exe file.

If you see the following error message

“Docker Desktop requires Windows 10 Pro/Enterprise (15063+) or Windows 10 Home (19018+).”

  • Update Windows by clicking on the "Update now" button here
  • Try installing docker again
  • Run the "D.exe file.
  • When prompted, ensure the Enable WSL 2 Features option is selected on the Configuration page

WSL2 error

  • If you encounter issues with WSL2, install "Linux kernel update package" from here

  • Start docker

    NOTE: search for Docker Desktip in the start menu.

  • When the whale icon in the status bar stays steady, Docker Desktop is up-and running, and is accessible from the Windows PowerShell

  • Open Windows PowerShell and run the following command to ensure that docker is working correctly
docker run hello-world

Once the docker is installed and running you can run qiime2 and fastqc via the following commands: 

docker run --rm -v ${pwd}:/data/ -w /data/ -it quay.io/qiime2/core:2023.5

For Mac Users:

1. Anaconda

  • Install Anaconda for Mac from here
  • Double click the .pkg file.
  • Test your installation.
  • Run the following command in the Terminal 
conda list

2. QIIME2

  • Run the following commands to install QIIME2

wget https://data.qiime2.org/distro/core/qiime2-2023.5-py38-osx-conda.yml
conda env create -n qiime2-2023.5 --file qiime2-2023.5-py38-osx-conda.yml
- activate QIIME2 environment

conda activate qiime2-2023.5
  • Run the following command to test the installation
qiime --help

2. FastQC

Download and install the following file.

Do you have issues starting the tool due to verification?

  • Install Java Development Kit from here and try again.

If installing Java Development Kit did not work, download the FastQC source code from here. Unzip the file and from the terminal window, navigate to the unzipped folder on your mac. Subsequently, run the following command: 

./fastqc