Biobb_Radiospineomics is a wrapped code for the extraction of conventional IVD features and radiomics from T2-weighted MRI
Project description
biobb_template
Introduction
Biobb_template is a complete code template to promote and facilitate the creation of new Biobbs by the community. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.
Version
v4.1.0 2023.4
Installation
If you have no experience with anaconda, please first take a look to the New with anaconda? section of the official documentation.
Download repository
Although the biobb_template repository is available at GitHub and thus you can clone it, we strongly recommend you to download it compressed and start your new project from scratch.
Create new conda environment
Once you have the project unzipped in your computer, please follow the next steps to create a new conda environment:
cd biobb_template-master
conda env create -f conda_env/environment.yml
Update environment paths
Edit conda_env/biobb_template.pth with the paths to your biobb_template folder. Example:
/home/user_name/projects/biobb_template/
/home/user_name/projects/biobb_template/biobb_template/biobb_template
Copy the edited conda_env/biobb_template.pth file to the site-packages folder of your environment. This folder is in /[anaconda-path]/envs/biobb_template/lib/python3.7/site-packages, where /[anaconda-path] is usually /anaconda3 or /opt/conda.
cp conda_env/biobb_template.pth /[anaconda-path]/envs/biobb_template/lib/python3.7/site-packages
Activate environment
Then, activate the recently created biobb_template conda environment:
conda activate biobb_template
Create repository
This template includes some folders not standard for a biobb, such as biobb_template/adapters/, biobb_template/notebooks/ or conda_env/. For the sake of having a pure biobb structure, you should uncomment the three last lines of the .gitignore file before creating a new git repository:
biobb_template/adapters
biobb_template/notebooks
conda_env
Then, inialitize repository:
git init
Binary paths configuration
Additionally, it's recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in the Binary path configuration section of the official documentation.
Run tests
To run tests, please execute the following instruction:
pytest /path/to/biobb_template/biobb_template/test/unitests/test_template/test_template.py
Or, if you prefer to show the BioBB output during the test process:
pytest -s /path/to/biobb_template/biobb_template/test/unitests/test_template/test_template.py
Documentation
Click here to find the API Documentation example for this template and here for Command Line documentation.
And here you can find the full documentation about how to build a new BioExcel building block from scratch.
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
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