- Core 2 Duo Processor or higher
- 4 GB DDR2 RAM or more
- Ubuntu 14.04 or later version
- Apache2
- PHP
- MySQL
- R & Shiny Server
- Bedtools
- php-common
- php-mysql
- Statistics::Basic
- File::Basename
UpSetR
corrplot
dplyr
SuperExactTest
shinythemes
shinyjs
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.