Validated Splicing Mutations Website

Description

A website which serves as a local interface to our Beacon API, allowing users to manually search for a variant, by gene name or genome coordinate range. It automatically queries our Beacon, and formats the results of the search, if any.

Steps to setup software for use

1) Extract files in this repository to a newly created Apache2 web root directory.
2) The placeholder 'BEACON_URL_PLACEHOLDER' appearing in js/searcharea.js must be replaced with the URL of your beacon API.
3) The placeholder 'PATH_TO_CONFIG_FILE_PLACEHOLDER' appears in multiple files and must be replaced with the path to a php config file you create containing credentials as follows:

$DBCREDS['beacon_dbuser_write_enabled'] = array(
        'host'          => '',
        'username'      => '',
        'password'      => '',
        'database'      => ''
);
$DBCREDS['beacon_dbuser_readonly'] = array(
        'host'          => '',
        'username'      => '',
        'password'      => '',
        'database'      => ''
);
$DBCREDS['beacon_table_name'] = '';

Usernames specified in beacon_dbuser_write_enabled and beacon_dbuser_readonly fields must have appropriate grants on the table specified by beacon_table_name.

4) Many files present in this repository reference CytoGnomix and other software tools created by CytoGnomix Inc. Manual modification of code is required to generalize the code for use by another organization or use-case.