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
> -----------------------------------------
>
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