The answer is. . . *now* the latest snapshot includes working changes for MacOS
as well.
The original changes were only tested on linux, and differences in the native
GUI libs required some extra alterations. Thanks for the debugging help :).
Anna Rissman
On 12/13/11, Roy Weckiewicz wrote:
> Hi,
>
> Thanks for working on this functionality!
>
>
> Does this latest snapshot include the change for MacOS as well? I tried with
> the latest snapshot (12-13) for mac 10.3 and I'm still getting the
> headless exception. This is the command I ran:
> >
>
>
> java -Djava.awt.headless=true -Xmx500m -cp /Volumes/Mauve\
> snapshot_2011-12-13/Mauve.app/Contents/Resources/Java/Mauve.jar
> org.gel.mauve.contigs.ContigOrderer \
> -output /Volumes/wolfa0001/a00test/${j}_headless \
> >
> -ref ref.fa \
> -draft assembly1.f.fasta
>
>
> Is this the same module as Mauve Contig Mover?
>
>
> Here's the exception I get:
>
>
> Exception in thread "main" java.awt.HeadlessException
> >
> at java.awt.dnd.DropTarget.<init>(DropTarget.java:79)
> at java.awt.dnd.DropTarget.<init>(DropTarget.java:125)
> >
> at
> com.apple.laf.AquaFileChooserUI.installListeners(AquaFileChooserUI.java:177)
> at com.apple.laf.AquaFileChooserUI.installUI(AquaFileChooserUI.java:123)
> >
> at javax.swing.JComponent.setUI(JComponent.java:662)
> at javax.swing.JFileChooser.updateUI(JFileChooser.java:1798)
> >
> at javax.swing.JFileChooser.setup(JFileChooser.java:360)
> at javax.swing.JFileChooser.<init>(JFileChooser.java:333)
> >
> at javax.swing.JFileChooser.<init>(JFileChooser.java:286)
> at org.gel.mauve.gui.AlignFrame.<init>(Unknown Source)
> >
> at org.gel.mauve.gui.ProgressiveMauveAlignFrame.<init>(Unknown Source)
> at org.gel.mauve.contigs.ContigMauveAlignFrame.<init>(Unknown Source)
> >
> at org.gel.mauve.contigs.ContigOrderer.init(Unknown Source)
> at org.gel.mauve.contigs.ContigOrderer.<init>(Unknown Source)
> >
> at org.gel.mauve.contigs.ContigOrderer.main(Unknown Source)
>
>
>
>
>
> Rgds,
> >
>
>
>
>
> Roy W.
>
> On Tue, Dec 13, 2011 at 2:49 PM, Anna Rissman <[email protected]
> <[email protected]>> wrote:
>
> > >
> >
> > >
> >
> > >
> > 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]
> > > <[email protected]>](java_script:main.compose()
> > >
> > > Sent: 02 December 2011 18:45
> > >
> > > To: Steven Platt
> > >
> > > Cc: [email protected] <[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]
> > > <[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] <[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. HTTP://www.HPA.org.uk
> > >
> > > **************************************************************************
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> > ------------------------------------------------------------------------------
> > >
> >
> >
> > Systems Optimization Self Assessment
> > >
> > Improve efficiency and utilization of IT resources. Drive out cost and
> > >
> > improve service delivery. Take 5 minutes to use this Systems Optimization
> > >
> > Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/
> > >
> >
> > _______________________________________________
> > >
> > Mauve-users mailing list
> > >
> > [email protected] <[email protected]>
> > >
> > https://lists.sourceforge.net/lists/listinfo/mauve-users
> > >
> >
> >
> >
>
>
>
> >
------------------------------------------------------------------------------
10 Tips for Better Server Consolidation
Server virtualization is being driven by many needs.
But none more important than the need to reduce IT complexity
while improving strategic productivity. Learn More!
http://www.accelacomm.com/jaw/sdnl/114/51507609/
_______________________________________________
Mauve-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/mauve-users
