Requirements¶

To run the pipeline you must install Nextflow. To use our Singularity container, you must install the Singularity package.

Nextflow¶

Local Computer¶

Before installing check your current version java -version. If return something as java version "1.X" and X is 8 up to 11, you can skip this step else install java.
Install Nextflow:

$> wget https://github.com/nextflow-io/nextflow/releases/download/v19.04.0/nextflow && chmod +x nextflow && \
echo 'export PATH=$PATH:'$(pwd) >> ~/.bash_profile && source ~/.bash_profile

High Performance computer (HPC)¶

Try module load java/1.8.0_121 or check with your administrator or on the HPC website.
Use wget to install Nextflow, change the name, add execution rights and add the Nextflow path in the bash_profile.

$> wget https://github.com/nextflow-io/nextflow/releases/download/v19.04.0/nextflow-19.04.0-all && \
mv nextflow-19.04.0-all nextflow && \
chmod +x nextflow && echo 'export PATH=$PATH:'$(pwd) >> ~/.bash_profile && source ~/.bash_profile

Singularity¶

Our Singularity container currently works on Linux. We highly recommend to use Singularity on a Linux local computer or on a HPC.

If you want to use Docker on Windows or MacOS, please see the Docker for TractoFlow section.

Local Computer¶

Install singularity-container. Our current singularity container works only on Linux. A macOS version will be released soon.

If you are Debian/Ubuntu, you can get neurodebian:

$> sudo wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list && \
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
sudo apt-get update && sudo apt-get install -y singularity-container

High Performance computer (HPC)¶

Please try module load singularity/3.5 or check with an administrator or on the HPC website.

Docker¶

MacOS¶

To install Docker on your MacOS computer, please check the following link:

https://hub.docker.com/editions/community/docker-ce-desktop-mac

Windows¶

To install Docker on your Windows computer, please check the following link:

https://hub.docker.com/editions/community/docker-ce-desktop-windows