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]> 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]
> ](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
> > > -----------------------------------------
> > >
> > ************************************************************************
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> >
> > --
> > Alex
> > -----------------------------------------
> >
> **************************************************************************
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