Installation¶
There are 2 ways to install and use p3. The first and recommended way for most users is to use the pre-built software containers available from Docker Hub and Singularity Hub. The second is to install p3 and all its dependencies natively.
Docker/Singularity¶
You can obtain the p3 container images by pulling from their respective repos on Docker Hub and Singularity Hub.
# You can replace 'latest' with the specific version you want
# Docker
docker pull p3proc/p3:latest
# Singularity
### Direct Singularity Image
singularity pull shub://p3proc/p3:latest
### Docker version for conversion; known to fail occasionally
singularity pull docker://p3proc/p3:latest
You can then run the pipeline with the run commands of Docker and Singularity.
# docker
docker run -it --rm p3proc/p3:latest
# singularity
singularity run p3proc_p3.simg
See the Usage section for more details on how to run p3.
Native Install (For Advanced Users and Developers)¶
The native install process for p3 is quite involved and generally not recommended for most end users. It is mainly intended for developers of p3 to debug the pipeline.
To use the native version of p3. It is recommended to have at least Python 3.6 and up. On Linux, the easiest way to obtain a copy is from your package manager, or to compile from Python Source. If you are on a Mac, the recommended way is through Homebrew.
After obtaining Python, you can install p3 in 2 ways. The first is to git clone the repo and install all the Python dependencies in requirements.txt.
# git clone the repo
git clone https://github.com/vanandrew/p3.git
cd p3
# you can use the --user flag to install locally; Make sure to use pip3.6+!
pip install -r requirements.txt
If you are testing with documentation, also install the requirements.txt under the docs.
# This installs the docs dependencies
pip install -r docs/requirements.txt
The other way is install p3 via pip.
# install via pip
pip install p3proc
Note that this method does not let you modify the source code/documentation.
Next you will need to install all of neuroimaging packages required by the default workflows in p3.
Follow the instructions for each respective package’s install page for your OS.
You will also need the bids-validator application which can be obtained through npm.
# This installs the bids validator globally
npm install -g bids-validator
This should allow you to run all default p3 pipeline workflows. See the Usage section for more details on running the pipeline.