Installation Instructions

Prerequisites

Installation of the NeuroDataPub has been facilitated through its distribution to the Python Package Index and the use of a conda Python 3.8 environment to install its dependencies, so in order to run NeuroDataPub, we would need to install Miniconda 3 (Instructions in Installation of Miniconda 3).

Once Miniconda 3 is installed, the recommended way to run NeuroDataPub is to use the NeuroDataPub Assistant. Usage instructions can be found in NeuroDataPub Assistant Guide. However, if you are not afraid by the creation of JSON files, or you feel more comfortable with the command-line interface, usage instructions for the neurodatapub command-line interface can be found in Running neurodatapub.

Installation of Miniconda 3

  • Download the installer of Miniconda 3 corresponding to your 32/64bits MacOSX/Linux/Win system from https://conda.io/miniconda.html. This can alternatively be done in the terminal:

    $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-<YOUR-OS>-x86_64.sh

  • Execute the downloaded script to install it:

    $ bash Miniconda3-latest-<YOUR-OS>-x86_64.sh

Note

NeuroDataPub has been tested only on Ubuntu and MacOSX.

Creation of neurodatapub-env conda environment

  • Download the appropriate conda environment.yml or environment_macosx.yml depending on your OS.

    Important

    It seems there is no conda package for git-annex available on Mac. For convenience, we created an additional environment_macosx.yml miniconda3 environment where the line - git-annex=[...] has been removed. Git-annex should be installed on MacOSX using brew i.e. brew install git-annex. See https://git-annex.branchable.com/install/ for more details.

  • Create the neurodatapub-env conda environment:

    $ conda env create -f /path/to/downloaded/environment[_macosx].yml

    This will create a Python 3.8 environment with all dependencies installed.

Installation of NeuroDataPub

Once the neurodatapub-env conda environment, NeuroDataPub can be installed in the neurodatapub-env conda environment via pip:

$ pip install neurodatapub

  • You are almost ready to use NeuroDataPub! You would need to have at least git-annex installed on the remote data server. Please see Remote Data Server Setup for instructions.

Help/Questions

Code bugs can be reported by creating a new GitHub Issue.