B+ is a database that has been specifically designed to store and show the information contained in ADOPS (Automatic Detection Of Positively Selected Sites) project files.
This project is an idea and is developed by:
- Jorge Vieira Molecular Evolution Group
- José Sousa i3S
- Miguel Reboiro-Jato SING Group
- Noé Vázquez González SING Group
- Bárbara Amorim i3S
- Cristina P. Vieira Molecular Evolution Group
- André Torres i3S
- Hugo López-Fernández SING Group
- Florentino Fdez-Riverola SING Group
N. Vázquez, C.P. Vieira, B.S.R. Amorin, A. Torres, H. López-Fernández, F. Fdez-Riverola, J.L.R. Sousa, M. Reboiro-Jato, J. Vieira (2018) Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects. Interdisciplinary Sciences: Computational Life Sciences: https://doi.org/10.1007/s12539-018-0282-7
N. Vázquez, C.P. Vieira, B.S.R. Amorin, A. Torres, H. López-Fernández, F. Fdez-Riverola, J.L.R. Sousa, M. Reboiro-Jato, J. Vieira (2017) On the automated collection and sharing (B+ database) of data on adaptive amino acid changes. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. Porto, Portugal
To install B+, the server must meet the following requirements:
- Web Server with PHP capabilities. For example, Apache >= 2.4.
- PHP >= 5.6.4.
- OpenSSL PHP Extension.
- PDO PHP Extension.
- Mbstring PHP Extension.
- Tokenizer PHP Extension.
- XML PHP Extension.
- Database Server. For example, MySQL Server 5.5.
- Database driver for PHP.
- Composer.
Clone B+ from GitHub (git clone https://github.com/sing-group/bpositive.git) or download a release version from here. Place all files in a directory you can use as document root of your web server.
The Web Server's document root must be the public directory of the B+ code. AllowOverride must be enabled in this directory.
The database and all the tables needed can be created using de SQL script included in database/sql/bpositive.sql.
Compressed files for each project must be stored under storage/app directory. By default, there is a disk named 'bpositive' configured to load files from app/bpositive, with this default configuration, files must be stored in storage/app/bpositive/files. Storage can be customized in config/filesystems.php.
All dependencies in B+ are managed using Composer. Just open a terminal on the root directory of B+ and run:
composer install
All the parameters can be customized in the .env file. At least, you need to customize the following parameters:
- APP_KEY: Make sure this key is set and remain secret.
- APP_DEBUG: If enabled, errors will be displayed on the client browser*
- APP_LOG_LEVEL: Sets the log level.
- APP_URL: URL where B+ will be runing.
- DB_CONNECTION, DB_HOST, DB_PORT, DB_DATABASE, DB_USERNAME, DB_PASSWORD: Database connection parameters.
Last but not least, directories within the storage and bootstrap/cache should be writable by the Web Server.
If you followed all the previous steps, B+ should be accesible from your Web Server root URL using any Web Browser with JavaScript enabled.
This project also enables the deployment of a B+ Environment in docker.
To run this project, first, you will need to install:
- Docker: https://www.docker.com/community-edition#/download
- Docker Compose: https://docs.docker.com/compose/install/
In order to build all the images use the following command inside the docker folder:
docker-compose build
In order to run all the images use the following command inside the docker folder:
docker-compose up
Once all the containers are up and running, the B+ web page will be available in the host IP and port 80. If you are running it locally, it will be available in http://localhost.
You can use the default admin user to log in and start uploading projects or create more users.
The default username is admin@bpositive and password bpositive.