Minimum System Requirements

• Core 2 Duo Processor or higher
• 4 GB DDR2 RAM or more
• Ubuntu 14.04 or later version

Tools & Dependencies

• Apache2
• PHP
• MySQL
• R & Shiny Server
• Bedtools

PHP Modules

• php-common
• php-mysql

Perl Modules

• Statistics::Basic
• File::Basename

R packages

UpSetR

corrplot

dplyr

SuperExactTest

shinythemes

shinyjs

Installation

Start by installing any HTTP server(Apache2) having support for server-side languages like PHP and configure accordingly. Install Bedtools, PHP, MySQL and R+ Shiny Server followed mentioned modedules/packages.

Clone (git clone https://github.com/sraghav-lab/BedSect.git)or download the Bedsect Github repositoy

Put all the contents from application folder to the Apache2 server root directory .

Create a database for Bedsect and import bedsect_schema.sql present in database_schema directory to the newly created database.

mysql -u <username> -p dbname<bedsect_schema.sql

To import the GTRD database schema use the gtrd_schema.sql file.

Update the database name, host, username and password in config.php file located in the root directory. The config file also contains default installation path and path to Shiny server, update the paths accordingly.

By default the email sending feature is disabled. To enable email sending first update SMTP served details in mail.php and remove comment form jobControl.php line no 25 and runJob.php line no 79.

Copy the contents of shiny folder to the Shiny server root directory. Default: /srv/shiny-server.

Change the user and group of the /var/www/html folder to www-data:www-data and set permission of the server/files folder to 755.

Navigate to localhost or server-ip-address and do a test run using the demo data provided in test_data folder.