In order to use Toppar you will need:
Instructions on how to install these dependencies on: MAC OS X.
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
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.):
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).
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 ...
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.
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.