Pre-course Instructions
Please follow these instructions to download all programs and data for the course. You will require ~1GB of space to install all programs and data.
Please create a new folder in which you will keep all the course materials and scripts (e.g., something like /Users/yourname/Documents/Workshop/ in Mac or Linux, or D:/Workshop/ in Windows).
Data and Scripts
Please download all data and scripts required for this course by clicking the following link (Note, the file size is ~ MB) and saving all the data and scripts contained in a folder on your computer.
Download Advanced Data and Scripts
Download Advanced Data and Scripts 2
Programs and software
Mac and Linux users
The easiest method for downloading all the software required for the workshop is to first download Miniconda.
Mac users, please follow these instructions:
- Open the Terminal.
- Enter the following code:
# Download and install Miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
# Follow prompts, then restart terminal
Linux users, please follow these instructions:
- Open the Terminal.
- Enter the following code:
# Download and install Miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
# Follow prompts, then restart terminal
Both Mac and Linux users:
Following the link to download the scripts above, you should have downloaded three scripts: Install_programs.sh, workshop_env.yml, and install_r_github.R.
These are the three scripts required to download all the programs required for the workshop.
- Open your terminal again.
- Navigate to the folder where you downloaded the scripts and data (e.g., /Users/yourname/Documents/workshop/):
- Run the following command:
- To activate the environment, run:
cd /Users/yourname/Documents/workshop/
bash Install_programs.sh
This may take up to 30 minutes, and you should now have a Conda environment called bioinfo-workshop and can run all the analysis from there.
source "$HOME/miniconda/etc/profile.d/conda.sh"
conda activate bioinfo-workshop
Windows users
For Windows users, it's a bit more involved to install Miniconda.
- Open PowerShell as Administrator and run:
- Install WSL2
- Install Ubuntu (default)
- Set up necessary components
- Restart your computer when prompted.
- After reboot, Ubuntu should open automatically. If not, open the WSL app manually. Wait for installation to complete, then choose a username and password when prompted. This opens a Linux terminal (Ubuntu shell).
- Enter the following commands to install Miniconda in WSL
- Accept the license agreement and confirm the default install location (e.g., /home/yourname/miniconda).
- When installation finishes, close and reopen WSL, or run:
- Check that Conda is available:
- Place the files (Install_programs.sh, workshop_env.yml, install_r_github.R) in a folder on Windows, e.g., D:/Workshop/.
- In the Ubuntu terminal, navigate to that folder:
- Enter the following command to set up a Conda environment and install programs usign Conda:
- To activate it type:
First, install WSL (Windows Subsystem for Linux)
wsl --install
This will:
Set up Ubuntu in WSL
Install Miniconda inside WSL
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh
You may get another prompt after this. Please type "no".
source ~/.bashrc
Export Conda into your path with:
export PATH=~/miniconda3/bin:$PATH
conda --version
Move Setup Scripts Into WSL
cd /mnt/d/Workshop/
Run the install script for Windows:
bash Install_programs_windows.sh
After up to 30 minutes, you should have a Conda environment called bioinfo-workshop set up and ready.
source ~/miniconda3/etc/profile.d/conda.sh
conda activate bioinfo-workshop
Windows users with ARM64 (alternative with Virtual Box)
Windows users with ARM64 operating systems can sometimes run into problems with downloading these programs and dependencies. If so, please following these instructions to run the workshop from a Virtual Box VM.
- Download Virtual box from https://www.virtualbox.org/wiki/Downloads.
- Install VirtualBox for your operating system.
- Download and install the Extension Pack from the same page (optional, for USB and folder sharing).
- Download Ubuntu Desktop 22.04 LTS (64-bit) from: https://releases.ubuntu.com/22.04/
- Choose: ubuntu-22.04.4-desktop-amd64.iso
- Open VirtualBox
- Click "New" and create a VM with the following settings:
- Name: BioinformaticsVM
- Type: Linux
- Version: Ubuntu (64-bit)
- Memory: at least 4096 MB (8192 MB recommended)
- Hard disk: dynamically allocated, 20 GB or more
- In "Settings → System → Processor", assign 2 or more CPUs
- In "Settings → Storage", attach the Ubuntu ISO to the optical drive
- Start the VM and follow the on-screen instructions to install Ubuntu
- Choose "Normal installation" and enable updates during install
- After installation, reboot and log into your new Ubuntu system
First, install Virtual Box
Download Ubuntu ISO
Create and Configure the Virtual Machine
Install Ubuntu
You should now be able to following the Windows instructions from step 4 above (Install Miniconda inside WSL) and work from within the VM.
All users
These programs must be installed directly from their websites:
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