Installing the pipeline - towbintools

Linux¶

For now, the pipeline was exclusively tested on Linux. There are not previous requirements before installing.

Clone the pipeline repo from github :

cd
git clone https://github.com/spsalmon/towbintools_pipeline.git

Install micromamba : BE CAREFUL, THE PIPELINE EXPECTS YOU TO CHOSE THE BASE OPTIONS AND YES ALL THE TIME. Then, restart your shell. You can skip this part if you already have it installed.

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)
source ~/.bashrc

Run the installation script :

cd ~/towbintools_pipeline
bash install_pipeline.sh

This will create a micromamba environment called towbintools, containing all required packages. Now you’re all set, click here to learn how to run your first pipeline. Click here to learn how to update the pipeline

Windows¶

You may have to install git first, follow instructions given here. For all the other steps, please run them using Git Bash (not CMD, not Powershell).
Using Git Bash, clone the pipeline repo from github :

cd
git clone https://github.com/spsalmon/towbintools_pipeline.git

Install micromamba, using Git Bash: BE CAREFUL, THE PIPELINE EXPECTS YOU TO CHOSE THE BASE OPTIONS AND YES ALL THE TIME. You can also ollow instructions given here

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

Then restart Git Bash manually.

Using Git Bash, run the installation script

cd ~/towbintools_pipeline
bash install_pipeline.sh

Another option is to use Windows Subsystem for Linux (WSL, follow instructions to install) and follow the Linux instructions inside of WSL.