Description

an Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies.

Usage

Usage Notes

Before running any OSGenome commands, a data directory included in the OSGenome application must be copied to the local directory you are running the commands from:

For Linux: cp -r /programs/x86_64-linux/osgenome/b05eae4/SNPedia/data ./

For Mac: cp -r /programs/i386-mac/osgenome/b05eae4/SNPedia/data ./

OSGenome on OSX requires XQuartz to use the DataCrawler_GUI interface. Download and install the latest Xquartz version offered on the MacOSForge site: https://www.xquartz.org.

The GUI interface to DataCrawler simply opens a File Choose dialog. It does not start the interactive web server for viewing results.

OSGenome contains its own python distribution within BioGrids. The python executable has been aliased to:

python.osgenome

OSGenome documentation indicates calling various python scripts :

python3 SNPedia/Datacrawler.py -f [Absolute path of your downloaded raw 23andMe data]

These scripts have also been aliased to just the name of the script (without .py):

python3 SNPedia/Datacrawler.py -f [Absolute path of your downloaded raw 23andMe data]

becomes:

Datacrawler -f [Absolute path of your downloaded raw 23andMe data]

The executable commands available in this way are:

DataCrawler DataCrawler_GUI GenomeImporter SnpApi

SnpApi opens a web server on the machine it is running on. A URL for localhost is displayed in the command line. In order to use this service on a remote host you will need to forward both graphics and ports.

Example run:

!/usr/bin/env bash

source /programs/biogrids.shrc

this_dir=$(pwd)

cp -r /programs//x86_64-linux/osgenome/b05eae4/SNPedia/data ./

DataCrawler -f ${this_dir}/genome_Daniel_Munro_Full_20141013190727.txt

echo "Run SnpApi to launch web server viewing app" SnpApi

Installation

Citation Note