For more information and advice on using this software please see the Artemis manual and our GitHub page. Also an Artemis poster gives an overview of browsing genomes and visualisation of next generation data in Artemis.
In addition, an email discussion list called artemis-users is available and posts to the list since September 2001 are archived at mail-archive.com
Frequently Asked Questions
Why does Artemis run out of memory on UNIX or GNU/Linux even though the machine has lots of memory?
The Java Virtual Machine (JVM) on UNIX has a fixed upper limit on the amount of memory that is available for applications, but this limit can be changed at runtime. As shipped Artemis will use a maximum of 2GB of memory.
You will need to change the art script to fix this problem. Find the line that reads: FLAGS="-mx2g -ms100m -noverify" and change the 2g (2 gigabytes) to a bigger number dependent on your machine memory (try 3g).
To change the memory allocated to Artemis on MacOSX, set the value in the file Info.plist in the directory Artemis.app/Contents. Towards the bottom of the file there are a couple of lines that look like this:
Changing the value after -Xmx will change the memory used by Artemis.
Why does Artemis run out of memory on Windows even though the machine has lots of memory?
Normally the Java virtual machine artificially limits the amount of memory that Artemis can use. The fix is as follows:
Create a shortcut to the Artemis JAR file. Edit the properties of the shortcut and add java -mx250m -jar to the start of the Target: field. -mx250m sets the maximum memory Java will allocate to Artemis. We recommend choosing a number that is about 50 megabytes less than the total amount of memory in the machine (to allow for the overhead of windows and the Java virtual machine).
You will need to use the shortcut to run Artemis from then on.
Launching Artemis from the web shows this message: 'Application Blocked by Security Settings'
As of the Java version 7u51 to launch Artemis from these pages the security settings need changing in the Java Control Panel. In the 'Security' tab select the button 'Edit Site List...' and add the following location to the list:
For more information see: Java Control Panel. Where is the Java Control Panel on my Mac? Where is the Java Control Panel on Windows?
Hints and Tips
Artemis and Hummingbird eXceed
If you use Artemis (or other java programs) with the Hummingbird eXceed X server for Windows you may have problems with borders disappearing. Hummingbird support told David Bauer to go to
exceed->xconfig->screen definition->set the window manager to "Native"
to force your x applications to use your operating system's window manager.
Artemis and ACT can be used to connect to Chado
databases. They are being developed to read from and write to the database and perform the same functions as the standard Artemis and ACT.
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