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 v21.10.6
for
illustrative purposes: newer versions might work or be required depending on the
pipeline at issue.
⚠️ Tractoflow is only compatible with nextflow
versions between 19.04.2 and 21.12.1 included. ⚠️
Local Computer
Before installing check your current version
java -version
. If return something asjava 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 nextflow/21.10.6
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 Alliance
Canada clusters, the above step might be substituted by adding the line
module load nextflow/21.10.6
(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 apptainer
. Our current singularity container works only on Linux.
$> sudo apt-get update && sudo apt-get install -y apptainer
High Performance computer (HPC)
Please try module load apptainer
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