Installation

Installation

Donut Falls uses containers to manage the tools used in its processes. This simplifies things for the end user (we promise).

Donut Falls needs

• nextflow (and nextflow's dependencies such as java and git)
• singularity or docker

Other container managers may also work, but we are not as familiar with those and may not be able to troubleshoot issues.

Nextflow

Nextflow has the most up-to-date installation instructions at https://www.nextflow.io/docs/latest/getstarted.html, but it is something like

wget -qO- https://get.nextflow.io | bash 
chmod +x nextflow

Java version 11+ is required for nextflow. More instructions are found here: https://www.java.com/en/download/help/download_options.html

sudo apt-get install openjdk-11-jdk

Docker

Docker requires root access and instructions can be found here: https://docs.docker.com/desktop/install/linux-install/

UPHL installed Docker via yum

sudo yum install -y yum-utils
sudo yum-config-manager \
    --add-repo \
    https://download.docker.com/linux/centos/docker-ce.repo
sudo yum install docker-ce docker-ce-cli containerd.io docker-compose-plugin
sudo systemctl start docker

Don't forget to follow the post-install instructions here: https://docs.docker.com/engine/install/linux-postinstall/

Singularity

Singularity installation instructions can be found here : https://docs.sylabs.io/guides/3.0/user-guide/installation.html

UPHL installed Singularity via yum

sudo yum update -y && \
    sudo yum groupinstall -y 'Development Tools' && \
    sudo yum install -y \
    openssl-devel \
    libuuid-devel \
    libseccomp-devel \
    wget \
    squashfs-tools

Pulling the workflow with Nextflow (recommended)

nextflow pull UPHL-BioNGS/Donut_Falls

Cloning this repo

The end user can also just clone this github repository, and use your local path.

# cloning this repo
git clone https://github.com/UPHL-BioNGS/Donut_Falls.git
# enabling easy updating
cd Donut_Falls && git init
# updating Donut Falls (while in the Donut_Falls' root directory)
git pull

Nextflow can then run this workflow from the cloned repository.

nextflow run <path to cloned repo>/Donut_Falls -profile singularity --sample_sheet <path to sample sheet>