Hi Charlie, thanks for the email - and sorry you had to fight to post to the list.
On 12/06/2013 20:21, Qiang Charlie Sun wrote: > I am adding some analysis tools including MSA to Pave and we decided > to use Jalview to visualize the results. One feature requested is > generating eps file for download. I installed the Jalview desktop > version and tried to run it in the command line mode to generate eps > file. Although I works on my local machine – a MBP running OSX 10.7 – > but it never works on our web server. It seems like it needs X11 > display to be enabled to run. Is there a way we can get around this? I'm afraid Jalview does need X on the server, since it relies on the X11 font libraries to render the alignment. However, you shoudn't need an X session active if the '-nodisplay' option is used. We also recommend you set 'java.awt.headless' to true in the system properties.. e.g.: java -Djava.awt.headless=true .. jalview.bin.Jalview -nodisplay -open ... This magic command line will also ensure that Jalview quits after generating the EPS, and is also documented in the FAQ (http://www.jalview.org/faq#server). The reason for this is that although Jalview tries to set the java.awt.headless flag when it gets the -nodisplay argument, on some JVMs we found that X was still required unless the property was set by the java binary. However, I did find another bug in Jalview which will prevent you using it on the server. This is documented at http://issues.jalview.org/browse/JAL-1315 and is now patched in the latest builds over at http://www.jalview.org/development/development-builds Hope this helps - and let me know if it doesn't! Jim. ps. Any support letters would be greatly appreciated - please do ask your manager! _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
