Data & Setup

Workshop Attendees

If you are attending one of our workshops, we will provide a training environment with all of the required software and data.
If you want to setup your own computer to run the analysis demonstrated on this course, you can follow the instructions below.

Data

You can download the data used in these materials as a zip file from dropbox.

Setup

Conda

We recommend using the Conda package manager to install your software. In particular, the newest implementation called Mamba.

To install Mamba, run the following commands from the terminal:

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh -b -p $HOME/miniforge3
rm Miniforge3-$(uname)-$(uname -m).sh
$HOME/miniforge3/bin/mamba init

Restart your terminal (or open a new one) and confirm that your shell now starts with the word (base). Then run the following commands:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda config --set remote_read_timeout_secs 1000

Nextflow

We recommend that you install Nextflow within a conda environment. You can do that with the following command:

mamba create -n nextflow -y nextflow

When you want to use Nextflow make sure to activate this software environment by running mamba activate nextflow.

Singularity

We recommend that you install Singularity and use the -profile singularity option when running Nextflow pipelines. On Ubuntu/WSL2, you can install Singularity using the following commands:

sudo apt install -y runc cryptsetup-bin uidmap
wget -O singularity.deb https://github.com/sylabs/singularity/releases/download/v4.0.2/singularity-ce_4.0.2-$(lsb_release -cs)_amd64.deb
sudo dpkg -i singularity.deb
rm singularity.deb

If you have a different Linux distribution, you can find more detailed instructions on the Singularity documentation page.

If you have issues running Nextflow pipelines with Singularity, then you can follow the instructions below for Docker instead.