About the Can’t connect to X11 window server error

[rspreafico]

Hello,

I am running Qualimap on Ubuntu server with no X11 installed. I was getting this error:

Exception in thread “main” java.lang.InternalError: Can’t connect to X11

window server using ‘xxxx:xx.0’ as the value of the DISPLAY variable.

As suggested in the FAQs (http://qualimap.bioinfo.cipf.es/doc_html/faq.html) I tried to unset the DISPLAY variable, as well as to assign it to :0 but neither worked for me.

Eventually after some Googling I found this fix: I edited the qualimap shell script and changed this line:

java $java_options -classpath $QUALIMAP_HOME/qualimap.jar:$QUALIMAP_HOME/lib/* org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain "${ARGS[@]}"

to (added the option in red):

java -Djava.awt.headless=true $java_options -classpath $QUALIMAP_HOME/qualimap.jar:$QUALIMAP_HOME/lib/* org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain "${ARGS[@]}"

This worked for me. Sharing this fix just in case somebody else runs into the same issue. Also, maybe would it be possible to include in future releases of Qualimap an explicit option for that?

Thank you for the awesome work!

Best,

Roberto

[Konstantin Okonechnikov]

Dear Roberto,

thanks a lot for this info!

I will update documentation for sure and perhaps also include a fix into the main script (as an option, for example).

Once this is done, I ll write again. 

--

  Konstantin

[Konstantin Okonechnikov]

Hi Roberto,

Qualimap documentation was updated:

http://qualimap.bioinfo.cipf.es/doc_html/faq.html#command-line

Also you are noted in the HISTORY file and last news message:

https://groups.google.com/forum/#!topic/qualimap/IXHeVN3XBjI

--

  Konstantin

On Friday, May 22, 2015 at 5:58:45 PM UTC+2, rspreafico wrote: