Hi I did make a request for this feature a while back and the response suggested the feature was being considered but wasn't trivial to implement.
http://www.mail-archive.com/[email protected]/msg00154.html Note that you can still run this from a script if you set up some kind of virtual frame-buffer to take the output, e.g. Xfvb and point $DISPLAY at that. Bit of a hack but it works. As long as the script runs without errors it doesn't actually use the screen for anything. If there's a problem you get a pop-up dialog. Cheers Nick On Tue, Dec 6, 2011 at 3:46 PM, Steven Platt <[email protected]> wrote: > Thanks Alex, > > It's more of a start than I would have made on my own. Unfortunately it > doesn't seem to work, producing errors like: > > Exception in thread "main" java.awt.HeadlessException > at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source) > at java.awt.Window.<init>(Unknown Source) > at java.awt.Frame.<init>(Unknown Source) > at java.awt.Frame.<init>(Unknown Source) > > I wouldn't know one end of java code from another (more of a perl/ruby > guy), but does this suggest that Mauve doesn't use awt? > > Anna: Is there a similar command for whatever graphical framework Mauve > uses? > > Thanks > > Steve > > -----Original Message----- > From: Alex Copeland [mailto:[email protected]] > Sent: 02 December 2011 18:45 > To: Steven Platt > Cc: [email protected] > Subject: Re: [Mauve-users] X11 problem when running cmd line contig > reordering > > 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. 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