TOPPAR

A browser for interactively viewing association results

Download Toppar »

Intro

Toppar is a database driven interactive association result browser written in JavaScript and HTML. It uses the Flot library for plotting, zooming and panning and DataTables for listing the data.


Toppar Online Version:

Features:

  • Association results from the GIANT consortium
  • Disease assocation from DISEASES
  • Association results from the GWAS catalog
  • Gene and exon annotations from Ensembl

Go to online version »

What does it do?

Main features:

  • Interactive and selective viewing of association test results attained from multiple resources
  • Incorporates GWAS catalog SNPs filtered by user specified terms
  • Display of gene, exon and variant annotation, highlighting genes already associated with disease

More details on Toppar's features »


Dependencies

In order to use Toppar you will need:

  • A Linux server running Apache configured to execute CGI scripts (should be installed by default).
  • An instance of the MySQL database, with an account with the privileges to create, drop and alter databases. (how to: MAC OS X)
  • The Perl DBD::mysql module. (how to: MAC OS X)

Instructions on how to install these dependencies on: MAC OS X.


Download

Downloading Toppar.

Get and untar the toppar software

$ wget https://github.com/totajul/toppar/raw/master/toppar_v1.tar.gz
$ tar -zxvf toppar_v1.tar.gz

## go to the toppar directory
$ cd toppar

Configuration

Configure Apache

Ask your web server administrator to create a web alias for the following directories (Or do it yourself (requires root access) following these Mac OS: instructions.):

  • toppar/cgi
  • toppar/web/json
Note!! Make sure that the web server has permission to execute files from the former directory (cgi) and permission to write to the latter (json).

Configure Toppar

Open the Toppar configuration file etc/config.txt in the Toppar directory and replace the bold text to suit your system:

$ vi etc/config.txt

## Replace xxx with your MySQL username and password ## the TopparWebAlias with your toppar web alias ## and the path2Toppar with the path to the directory where you saved the toppar software ## If you want to upload and delete data from the Toppar GUI, you also have to replace path2MySQL with the full path to mysql on your system.

## mysql database=toppar_01 user=xxx password=xxx dsn=DBI:mysql:database TOPPAR_WEB=TopparWebAlias TOPPAR_HOME=path2Toppar mysql=/path2MySQL/mysql genome_build=GRCh38

For example, on my system the file looks like this:

## mysql
database=toppar_01
user=tota
password=myPw
dsn=DBI:mysql:database

TOPPAR_HOME=/Users/tota/repository/toppar
TOPPAR_WEB=http://localhost

mysql=/usr/local/mysql/bin/mysql

...
	

Quick start using GIANT data

Create and populate the Toppar database with a subset of GIANT 2015 data.

#go to he topppar directory
$ cd toppar

#run the giant initiation script
$ sh init_with_giant.sh

Note that this is an interactive script and you have to reply "yes" twice for it to complete fully.

More detail on the commands within the init_with_giant.sh script can be found here.

After running the script you should be able to view the GIANT subsets, GWAS catalog data, gene, exon and disease annotations in the Toppar browser.


Contact

Tota Juliusdottir
toppargb@gmail.com

License


Copyright 2017 Thorhildur Juliusdottir
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.