I ran into a similar problem with MEGAN a while back. I am no java jockey, so I don't know if the fix for MEGAN will work for you, but the workaround in that case was to create a .vmoptions file containing -Djava.awt.headless=true .
At the risk of providing too much information, I'll add that MEGAN itself is a wrapper script that goes to great pains to sort out what jvm , classpath, megan binary, vmoptions, etc., etc,. to use, so that by creating a copy of the wrapper called, say, 'megan-headless' and an accompanying .vmoptions file called 'megan-headless.vmoptions' the startup process arranges for the correct .vmoptions file to be read. Then the magic of the java.awt.headless=true flag can work. I suppose this idea is DOA if mauve doesn't use awt, but perhaps a similar trick would apply for other windowing libs if needed. HTH On Thu, Dec 1, 2011 at 6:48 AM, Steven Platt <[email protected]> wrote: > Hi, > > I'm trying to get Mauve Contig Mover (MCM) to run from the command line > using the following infrastructure and command: > > Infrastructure: mauve_2.3.1 on an x86 64bit linux server (X11 enabled), > accessed via an SSH client from a windows desktop. > > Command: java -Xmx500m -cp ~/bin/mauve_2.3.1/Mauve.jar > org.gel.mauve.contigs.ContigOrderer -output 3kb_20_reordered -ref > H063920004_ref_genome.gbk -draft 3kb_20_k41_final.scaffolds.fasta > > Initially there was an X11 error "No X11 DISPLAY variable was set, but > this program performed an operation which requires it.". > So I switched to a different SSH client that allows X11 forwarding and > got "Can't connect to X11 window server using 'localhost:10.0' as the > value of the DISPLAY variable." > We solved this by installing Xming (a windows X server > http://www.straightrunning.com/XmingNotes/) on the desktop PC and now > MCM runs as expected. > It looks like MCM is trying to initiate a graphical process even though > it's run from the command line... > > So what's the problem?... > > We want to run MCM as part of a pipeline of tools served through an > online interface. Requiring the integration of X servers on user > desktops is obviously a show stopper. > > Questions: Should MCM be invoking a graphical component when run from > the command line? Is there any way of preventing it? > > Thanks > > Steve > Bioinformatics > Health Protection Agency > UK > ----------------------------------------- > ************************************************************************** > The information contained in the EMail and any attachments is > confidential and intended solely and for the attention and use of > the named addressee(s). It may not be disclosed to any other person > without the express authority of the HPA, or the intended > recipient, or both. If you are not the intended recipient, you must > not disclose, copy, distribute or retain this message or any part > of it. This footnote also confirms that this EMail has been swept > for computer viruses, but please re-sweep any attachments before > opening or saving. HTTP://www.HPA.org.uk > ************************************************************************** > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Alex ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
