Hi all.
Between Aaron and I, we think we've managed to put together a version of Mauve Contig Mover that should work friendlily with the Java headless mode. While we don't currently have a formal release planned, the latest snapshot should have the added functionality, and can be found at: http://gel.ahabs.wisc.edu/mauve/snapshots/. Hope this helps. . . and sorry for the wait to those who have requested this previously. Anna Rissman On 12/06/11, Steven Platt 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]](javascript:main.compose() > 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. 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 > ----------------------------------------- > ************************************************************************** > 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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