Roslin Bioinformatics - Genotype Checker

Running the Application

This Java application requires the current Java Virtual Machine (Java 1.6 aka Java6) to be installed on your local Windows, Linux or Mac machine. Users of Macintosh systems should note that Java6 is only available for Mac OS X 10.5 upwards. The application is distributed as a single 'jar' file and can be run on Windows simply by double-clicking on this file. It can be started on a Linux or Windows terminal by executing the following command line from within the same directory as the jar file (or adding the appropriate relative path to the file name).

   java -jar GenotypeChecker[version#].jar

or using flags to increase the memory used (2G in this example)

   java -jar -Xmx2048m -Xms512m -XX:+UseParallelGC GenotypeChecker[version#].jar

Increasing the memory available to the application is important when processing large data files with hundreds of individuals and scores of markers. The application runs in the context of your machine, so that the File Picker for loading or saving files should default to your home directory. Similarly Printing commands should access your available printer list (which may take some time on a Windows machine!).

Run using Java Web Start

The Web Start links on the download page automatically install and start the application, using alternate memory parameters. Once installed locally the application can be run from you machine, and automatically checks for updates if connected to the internet.

Run using scripts

To simplify the running of GenotypeChecker three separate script files are supplied (see Download), one each for Linux, Windows or Mac, which should be copied to the same directory as the downloaded application. These scripts start the application with optimized memory usage. The scripts are run from the command line (e.g. './linuxRunme.sh &') or the Windows batch file can be executed by double clicking 'windowsRunme.bat'. For Macs we also supply an archived App file 'ResspeciesGenotypeChecker.app.'

NOTE

32-bit Windows machines will not access more than 1G of RAM. It is recommended for large datasets that you run GenotypeChecker on a *NIX architecture; 64-bit Windows may allow higher memory utilization (untested).