Fast Installation¶

Easy install method¶

Enter this command in your terminal (it downloads the container and TractoFlow code in the current directory - Make sure nextflow is already installed before running this command):

curl -s https://tractoflow-documentation.readthedocs.io/en/2.4.0/install.sh | bash

Detailed Installation¶

TractoFlow pipeline¶

Release¶

Download TractoFlow pipeline:

$> nextflow pull scilus/tractoflow

For developers¶

Clone TractoFlow pipeline repository:

# Clone with HTTPS
$> git clone https://github.com/scilus/tractoflow.git

# Clone with SSH
$> git clone git@github.com:scilus/tractoflow.git

As a developer you will have to run tractoflow using this command:

nextflow run tractoflow/main.nf --help

Singularity for TractoFlow¶

Release¶

Download the last release of the Singularity container for TractoFlow:

$> wget http://scil.usherbrooke.ca/containers_list/scilus_1.4.0.sif

Or if you have sudo privileges

$> sudo singularity build scilus_1.4.0.sif docker://scilus/scilus:1.4.0

For developers¶

Clone the singularity repository for TractoFlow pipeline:

# Clone with HTTPS
$> git clone https://github.com/scilus/containers-scilus.git

# Clone with SSH
$> git clone git@github.com:scilus/containers-scilus.git

Then, you can build the singularity image:

$> singularity build scilus_1.4.0.sif singularity_scilus.def

Docker for TractoFlow¶

First, change the number of CPUs and RAM (recommended: 8 CPUs and 16Gb of RAM) in Docker (Preferences -> Advanced) and click on Apply & Restart.

Download the last release of the Docker container for TractoFlow:

$> docker pull scilus/scilus:1.4.0

Please see Profiles section to use macos profile.