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B+ A database of Positively Selected Sites discovered with ADOPS
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README.md

B+

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.

Team

This project is an idea and is developed by:

If you use B+, please cite us:

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

Downloading and Installing B+

0. Prerequisites

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.

1. Download

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.

2. Web Server configuration

The Web Server's document root must be the public directory of the B+ code. AllowOverride must be enabled in this directory.

3. Data cofiguration

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.

3. Install

All dependencies in B+ are managed using Composer. Just open a terminal on the root directory of B+ and run:

composer install

4. B+ configuration

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.

5. B+ Web Page

If you followed all the previous steps, B+ should be accesible from your Web Server root URL using any Web Browser with JavaScript enabled.

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