Roslin Bioinformatics - VIPER

Running the Application

This Java application requires a relatively recent version of the Java Virtual Machine (Java 1.6 aka Java6 or JRE1.6) to be installed on your local Windows, Linux or Mac machine. However, this is provided as standard for most desk-top user environments. Users of Macintosh systems should note that Java6 is only available for Mac OS X 10.5 upwards.

Web Start

The application is provided via automatic Web Start links on the download page, which vary according to the amount of memory available to the user (1.0, 1.5, 2.0, 2.5, 3.0 etc.). 32-bit Windows machines will not allow Java to access more than 1G of RAM. It is recommended for large datasets that you run VIPER on 64-bit Windows, or a *NIX architecture (including Mac OSX). Web Start should install desktop links for starting VIPER and once downloaded VIPER can be run locally and will check online for available updates.

However, Windows 64-bit users may still experience problems running VIPER with high memory, typically because both 32 bit and 64 bit versions of Java are installed on your machine, and JNLP applications are being wrongly associated with the 32 bit version. This can be difficult to resolve. For example you may see that the .jnlp file or shortcut is associated with 'C:\Program Files (x86)\Java\jre6\javaws.exe' (or 'C:\Windows\SysWOW64\javaws.exe') instead of the correct 'C:\Program Files\Java\jre6\javaws.exe' . If this happens and is not easily resolved it is best to run the JNLP directly with the correct 64-bit version of javaws.exe via the command line, using the appropriate downloaded .jnpl file (viper_1.0.jnlp, viper_3.0.jnlp etc.). This will also ensure that the VIPER web start version is kept up to date.

e.g.

path_to_64bit/javaws.exe viper_3.0.jnlp

Alternatively the VIPER application can be downloaded as a complete JAR and run with full user control via the command line as described below. However, unlike with Web Start this JAR will not be automatically updated when future releases of VIPER become available.

Running VIPER as a bundled jar

We provide a large VIPER (complete) bundle JAR that contains all the dependencies required to run from the command-line, allowing the user to set memory parameters as required: VIPER-[version]-jar-with-dependencies.jar.

e.g.

java -jar -Xmx1G -Xms1G VIPER-[version]-jar-with-dependencies.jar

The application could also be run from the non-bundled JARs from command line or with user defined scripts, the minimal required JARs on the class path are:

i.e.

java -jar -Xmx1G -Xms1G Pedigree-[version].jar

Note that this depends on the manifest file in Pedigree-[version].jar listing the other JARs on the classpath (which is requires all the JARs to be in the same directory as the Pedigree.jar). It is possible to override the manifest classpath of a jar using a local classpath (use colons on *NIX rather than semi-colons):

e.g.

java -Xmx1G -Xms1G -cp resspecies-lw-inheritance-1.06.jar;resspecies-datasourceaware-1.2.jar;resspecies-datasourceaware-interface-1.1.jar;resspecies-model-1.1.jar;commons-collections-3.2.jar;JSwingPlus-[version].jar;Pedigree-[version].jar napier.pedigree.Test

Additional JARs are required if the user wants the ability to save PDF or SVG graphics (see here).

Mac OSX

We also provide a compressed zip archive of VIPER.app for installing and running on Apple Mac OSX machines.