Once you’ve installed conda, initialize a new conda environment (for example, named
cubids) as follows:
$ conda create -n cubids python=3.8 $ conda activate cubids
You are now ready to install CuBIDS. You can do so in one of two ways.
CuBIDS locally, we can use
pip to download our software from the
Python Package Manager (Pypi) by running the following commands:
$ pip install CuBIDS
Alternatively, you can clone the source code for
CuBIDS from our GitHub repository
using the following command:
$ git clone https://github.com/PennLINC/CuBIDS.git
Once you have a copy of the source, you can install it with:
$ cd CuBIDS $ pip install -e .
We will now need to install some dependencies of
CuBIDS. To do this, we first must install
nodejs. We can accomplish this using the following command:
$ conda install nodejs
Now that we have npm installed, we can install the
bids-validator using the following command:
$ npm install -g firstname.lastname@example.org
In our example walkthrough, we use
bids-validator v1.7.2. using a different version of the
validator may result in slightly different validation tsv printouts, but
CuBIDS is compatible with all
versions of the validator at or above v1.6.2.
We also recommend using
CuBIDS with the optional
DatLad version control capabilities.
DataLad throughout our walkthrough of the CuBIDS Workflow on the Example Walkthrough page.
To leverage the version control capabilities, you will need to install both
the large file storage software
DataLad runs under the hood. Installation instructions
git-annex can be found here