Roslin Bioinformatics - ArkMAP- Java and WebStart Help

Java and Web Start system requirements

The ArkMAP desktop application is written in the platform independent language Java, and requires that a Java Runtime Environment (JRE) of at least version 1.6 is installed on your computer. ArkMAP uses Java Web Start technology to allow single click deployment over the Internet. Java Web Start (javaws) ensures that the most current version of the application will be deployed, as well as the correct version of the JRE. Once installed on your machine, version updates of ArkMAP are automatically retrieved. You can check whether your Internet browser (Chrome, Firefox, IE, Safari etc.) is configured to use the JRE plug-in using the button below. Further browser settings may be necessary (see below).

It is preferable to use a 64 bit version of Java as this gives access to higher system memory - this is only possible on machines with 64 bit operating systems. The Java download pages will guide you through the installation issues, which are complicated by the fact that many browsers are still 32-bit and require a 32-bit Java plug-in. 


Most users will be using a 64-bit version of Windows, but may be using 32-bit versions of the browsers (Firefox, IE, Chrome...). These will install the 32-bit java plug-in which will run ArkMAP with a maximum of 1G RAM. If you want to use more memory for larger queries and maps, choose to install the 64 bit version of Java in addition, and then manually associate Java Web Start ('.jnlp') file types with javaws.exe (e.g. use Start/Default Programs/Associate File Type .jnlp = C:\Program Files\Java\jre6\bin\javaws.exe i.e. do not use the 32-bit version in 'C:\Program Files (x86)\Java\...' or aliased in the 'C:\Windows\SysWOW64' folder).

Corrupt Desktop Shortcuts

Installing both 32- and 64-bit versions of Java is probably unavoidable until 64-bit versions of browsers are available, but causes notorious confusion to Windows, Applications and Users! In particular any desktop links created by WebStart may point at the wrong Java. This can be corrected by editing the shortcut's properties to change the 'Target' from C:\Windows\SysWOW64\javaws.exe ... to C:\Windows\System32\javaws.exe ... or even more specifically C:\Program Files\Java\jre6\bin\javaws ...

Alternately, run javaws or java on the command line (see below) to manually control which version of Java that you run. 


For Java versions 6 and below, Apple supplies their own version of Java. For Mac OS X 10.6 and below, use the Software Update feature (available on the Apple menu) to check that you have the most up-to-date version of Java 6 for your Mac. Java 7 requires an Intel-based Mac running Mac OS X 10.7.3 (Lion) or later and administrator privileges. A 64-bit browser (Safari or Firefox, for example) is required to run Java 7 on Mac OS X. 32-bit browsers such as Chrome do not support Java 7 on the Mac platform, however, upon downloading a '.jnlp' file with Chrome you may associate javaws application with these file types.

NOTE: From MAC OS X.8 Apple have introduced default 'GateKeeper' Security to prevent users running applications that have not purchased an annual licence from Apple....

Your system may let you run ArkMAP using 'admin' credentials, or you can resolve this issue:

  • click on the Apple Menu -> System Preferences -> Security & Privacy.
  • On the General tab, click the lock icon in the bottom left to allow for changes.
  • You will be prompted for your password.
  • Finally, set it to "Allow apps downloaded from: Anywhere"
show example



32 and 64-bit versions of JRE 1.6 and 1.7 are available from Oracle, note that the JRE provided by the 'openjdk' project does not include javaws. 

Browser Settings

Even after Java has been installed on your machine it may sometimes be necessary to individually configure browsers to auto-start Web Start ('.jnlp' file) downloads.

use the Options (a.k.a. Preferences)/Applications menu

Program associations (auto-opening settings) are made upon file download (i.e. JNLP files are associated with Java Web Start) - these settings can be cleared at chrome://chrome/settings/ +Show advanced settings/Downloads

Internet Explorer
file associations are shared with Windows Default Programs as described above

enable 'Open "safe" files' on Preferences/General menu

File associations are made upon download, these are cached but can be cleared or edited in Preferences/Advanced/Downloads (associate MIME type application/x-java-jnlp-file : jnlp extension : /System/Library/CoreServices/Java Web Start)


Web Start still not working?

Look at this Java help site.

Try any of these approaches:

  • Download the .jnlp file, and click on it to run.
  • Download the .jnlp file, then start it on the command line:
  • > javaws arkmap-jensembl.jnlp
    > javaws arkmap-jensembl64.jnlp
  • Download and run directly on the command line: > javaws
    > javaws

Note: You may want to specify the full path to the version of javaws in order to ensure that the correct version is used, for example: > "C:\Program Files\Java\jre6\bin\javaws" arkmap-jensembl64.jnlp

Give up on Web Start

We provide ArkMAP installers for both Windows and Mac executables. We also provide a single JAR archive file. However, if you choose to use the non WebStart options you should regularly check this page for new release versions of ArkMAP. This is particularly important because each new release of the Ensembl databases may require configuration changes to the JEnsembl API. (Typically Ensembl release new data versions every three months).