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marcelzwiers committed Oct 18, 2023
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Installation
============

BIDScoin can be installed directly on your operating system, or can be installed in a so-called container. Direct installation is arguably simpler and lighter, but containerized installations are better guaranteed to always work and be reproducible. Below you find instructions for direct installation, followed by instructions for installation in a container. Alternatively, if you like to use a container but don't like the complexity of its overhead, you can install `NeuroDesk <https://www.neurodesk.org/>`__ and use the pre-installed BIDScoin container without needing to know anything about containers.
BIDScoin can be installed directly on your operating system, or in a so-called container. Direct installation is arguably simpler and lighter, but containerized installations are better guaranteed to always work and be reproducible. Below you find instructions for direct installation, followed by instructions for installation in a container. Alternatively, if you like to use a container but don't like the complexity of its overhead, you can install `NeuroDesk <https://www.neurodesk.org/>`__ and use its pre-installed BIDScoin container without needing to know anything about containers.

Python installation
-------------------
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$ sudo docker build -t bidscoin .
Alternatively, you can pull a pre-build image from Docker hub

.. code-block:: console
$ sudo docker pull marcelzwiers/bidscoin:<version>
Run BIDScoin tools in the container
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Executing BIDScoin commands via Docker is less simple than via Apptainer (and surely less simple than running them directly on your host computer). For instance, it is typically needed to bind-mount your data folder(s) in the container and, for the bidseditor, to bind-mount an x-server socket to display the GUI in your host computer. The syntax to run dockerized bidscoin tools is:

.. code-block:: console
$ docker run --rm -v <bind_mount> bidscoin <bidscoin_tool> <bidscoin_tool_args>
$ docker run --rm -v <bind_mount> bidscoin <bidscoin_tool> <bidscoin_tool_args> # If you built the image from the Dockerfile
$ docker run --rm -v <bind_mount> marcelzwiers/bidscoin:<version> <bidscoin_tool> <bidscoin_tool_args> # If you pulled the image from Docker hub
If you have source data in ``/my/data/raw``, instead of running ``bidsmapper /my/data/raw /my/data/bids`` and then ``bidsmapper /my/data/raw /my/data/bids``, you now execute for instance:

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