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# 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](http://biobb_template.readthedocs.io/en/latest/).
## Version v3.0.0 2021.3
## Installation
If you have no experience with anaconda, please first take a look to the [New with anaconda?](https://biobb-documentation.readthedocs.io/en/latest/first_steps.html#new-with-anaconda) section of the [official documentation](https://biobb-documentation.readthedocs.io/en/latest/).
### 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](https://github.com/bioexcel/biobb_template/archive/master.zip) 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:
`console
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:
`console
/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.
`console
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:
`console
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:
`console
biobb_template/adapters
biobb_template/notebooks
conda_env
`
Then, inialitize repository:
`console
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](https://biobb-documentation.readthedocs.io/en/latest/execution.html#binary-path-configuration) section of the [official documentation](https://biobb-documentation.readthedocs.io/en/latest/).
## Documentation
[Click here to find the API Documentation example](https://biobb-template.readthedocs.io/en/latest/template.html) for this template and [here for Command Line documentation](http://biobb_template.readthedocs.io/en/latest/command_line.html).
And here you can find [the full documentation](https://biobb-documentation.readthedocs.io/en/latest/) about how to build a new BioExcel building block from scratch.
## Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
2015-2020 [Barcelona Supercomputing Center](https://www.bsc.es/)
2015-2020 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
