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.