Thanks for replying! I believe we are using Sun JDK. This is what's
returned when I enter the command "java -version":
java version "1.7.0_06"
Java(TM) SE Runtime Environment (build 1.7.0_06-b24)
Java HotSpot(TM) 64-Bit Server VM (build 23.2-b09, mixed mode)
This is the version I used when I got the errors from my previous email.
Exactly which version of a Java VM will make this work? Also, please let
me know if/when there is any development towards fixing this problem.
Thanks again!
-Julie
On 12/08/2014 11:00 AM, Aaron Darling wrote:
Hi Julie, apologies for the delayed response.
Matt DeMaere here at UTS has looked into this issue and it appears to be
a problem specific to recent versions of OpenJDK. Whereas the code will
work command-line on the Sun Java VM without an X11 environment, the
OpenJDK implementation of Java library functions used by the contig
mover still require an X11 display. We are looking into how this can be
fixed. In the meantime it's possible to work around the issue by using a
Sun JDK or with the rather hackish approach of creating an X11
environment on the server with, e.g. VNC, that the contig mover can
silently connect to.
Best,
-Aaron
On Wed, 2014-07-16 at 06:59 +1000, Julie Shay wrote:
Hi Aaron,
Thanks so much for your quick response. I know that Mauve is great for
genome alignments, and I find the contig mover very useful, which is
why I want to incorporate it into this pipeline. My coworkers and I
have tried to run the contig mover with both the most recent snapshot
and with snapshots shortly following the post I linked below, and we
keep getting similar errors. Here is an example of a command we've
been trying and the errors we've been getting:
java -Djava.awt.headless=true -Xmx500m
-cp /home/jshay/Programs/mauve/mauve_snapshot_2011-12-16/Mauve.jar
org.gel.mauve.contigs.ContigOrderer -output 0093mauvetest -ref
0093.gbk -draft 0093spades/contigs.fasta
Exception in thread "main" java.lang.NullPointerException
at
javax.swing.JFileChooser.isTraversable(JFileChooser.java:1596)
at
javax.swing.JFileChooser.setCurrentDirectory(JFileChooser.java:575)
at javax.swing.JFileChooser.<init>(JFileChooser.java:344)
at javax.swing.JFileChooser.<init>(JFileChooser.java:296)
at org.gel.mauve.gui.AlignFrame$1.<init>(Unknown Source)
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)
Do you know of something we might be doing wrong on our end? If we get
this to work, we can use a snapshot and reference the date stamp as
you suggest. Thanks again!
-Julie
On 13/07/2014 7:43 PM, Aaron Darling wrote:
Hi Julie,
There will be another release with a traditional numeric version
identifier eventually, but as it currently stands the development
snapshots are about as "stable" as research software gets. There are a
number of cosmetic bugs but no major bugs that I am aware of in terms of
the calculation of genome alignments. If you want to incorporate to your
pipeline, I would suggest referencing the datestamp as the software
version -- the snapshots will remain available to the public so that
reproducibility of results by others can be achieved by obtaining a
matching datestamped build of the software.
Best,
-Aaron
On Fri, 2014-07-11 at 04:32 +1000, Julie Shay wrote:
Hi,
Are there currently any plans for an official release of a Mauve
update? We would like to use the Mauve Contig Mover from the command
line on our lab's cluster without an X-display, and I see that you've
done an unofficial update that allows this
(http://sourceforge.net/p/mauve/mailman/message/28484265/ ), but I
was wondering whether your plans regarding a formal release have
changed in the past 2.5 years? We're trying to integrate the Mauve
Contig Mover into one of our pipelines, and we want to be confident
that the version we use is stable. Thanks!
-Julie
--
Julie Shay
Graduate Student
Brinkman Laboratory, MBB Department
Simon Fraser University, Burnaby, B.C., Canada, V5A 1S6
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