Requirements¶

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

Nextflow¶

Note that the below sections use nextflow version v19.04.0 for illustrative purposes: newer versions might work or be required depending on the pipeline at issue.

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:

$> wget https://github.com/nextflow-io/nextflow/releases/download/v21.10.6/nextflow && chmod +x nextflow && \
echo 'export PATH=$PATH:'$(pwd) >> ~/.bash_profile && source ~/.bash_profile

High Performance computer (HPC)¶

Try module load nixpkgs/16.09 module load java/1.8.0_192 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.

$> wget https://github.com/nextflow-io/nextflow/releases/download/v21.10.6/nextflow-21.10.6-all && \
mv nextflow-21.10.6-all nextflow && \
chmod +x nextflow && echo 'export PATH=$PATH:'$(pwd) >> ~/.bash_profile && source ~/.bash_profile

Note that a given HPC system might offer (a) readily available nextflow version(s). If any of provided versions suffice for the pipeline at issue, the above step can be omitted, and reading the documentation of the HPC system is encouraged in order to load the suitable version. In the case of the Allianca Canada clusters, the above step might be substituted by adding the line module load nextflow/19.04.0 (depending on the desired and available versions) to the .bash_profile file and sourcing it.

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

Note that the first command contains the OS codename xenial (corresponding to Ubuntu 16.04) as an example; if your OS is different, you will need to retrieve the corresponding type/version from the menus in https://neuro.debian.net/index.html#get-neurodebian so that you can use the appropriate URL for the wget command.

High Performance computer (HPC)¶

Please try module load singularity/3.7 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