Unfortunately, these instructions will only work with MacOS and Linux systems. Windows users will need to just follow along.
Please see the official installation instructions for your system
If you haven't already, you will need to install Python with pip and virtualenv packages on your system. There are many ways to do this, which depend on your OS. A comprehensive guide can be found here.
In most casees, the above instructions will also install pip and virtual env, but if you
are on Linux you may also need to install the packages separately, e.g. sudo apt install python3-pip.
Next we will install a package called xnat4tests that enables you to run your own
XNAT instance. It can be installed with
python3 -m venv ~/xnat4tests.venv
source ~/xnat4tests.venv/bin/activate
pip install xnat4tests
xnat4tests start
NB: It will take some time to build the Docker image, and then more time again to launch it, ~5 min in total
Type http://localhost:8080 into your browser and then login to XNAT using the username admin and password admin
Xnat4Tests can also generate/download sample data to populate the test XNAT. There are currently 3 sample datasets, "simple-dir", "openneuro-t1w" and "dummydicom". They can be installed with
xnat4tests add-data simple-dir
xnat4tests add-data openneuro-t1w
xnat4tests add-data dummydicom
git clone https://github.com/Australian-Imaging-Service/pipelines-community
python3 -m venv ~/pipelines.venv
source ~/pipelines.venv/bin/activate
cd ./pipelines-community
pip install -r requirements.txt
To build the edited specifications, run the following command from your virtualenv from the pipelines-community repository you cloned
arcana deploy make-app ./australian-imaging-service-community xnat:XnatApp --loglevel info --build-dir ~/pipelines-build-dir --use-test-config