Roslin Bioinformatics - ArkMAP- Java and WebStart Help
- Java Web Start system requirements
- Browser Settings
- Web Start still not working?
- Give up on Web Start - Download the complete application
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"
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.
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
- Download and run directly on the command line:
> javaws http://www.thearkdb.org/webstart/arkmap-jensembl.jnlp
> javaws http://www.thearkdb.org/webstart/arkmap-jensembl64.jnlp
> 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).