Supported Applications

OSGenome

  • Description

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

  • 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

    Use the following command to install this title with the CLI client: $ biogrids-cli install osgenome Copy to clipboard
  • Citation Note

    https://github.com/mentatpsi/OSGenome

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