Details
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Type: Bug
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Status: Resolved
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Priority: Critical
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Resolution: Fixed
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Affects Version/s: 2.2.1
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Fix Version/s: 2.3
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Component/s: None
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Labels:None
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Mantis ID:21530
Description
Bug reported by Paco Hulpiau.
Hello
I'm having problems running Jalview on our server.
The following doesn't work (need to use Jalview in cgi-script for a tool with webinterface):
command:
java -Djava.awt.headless=true -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -nodisplay
-open [aln-file] -png [png-file]
result:
Java version: 1.4.2_06
i386 Linux 2.6.9-42.0.10.ELsmp
Jalview Version: 2.2.1
Opening file: [aln-file]
java.awt.HeadlessException
at java.awt.dnd.DropTarget.<init>(Unknown Source)
at java.awt.dnd.DropTarget.<init>(Unknown Source)
at jalview.gui.AlignFrame.init(Unknown Source)
at jalview.gui.AlignFrame.<init>(Unknown Source)
at jalview.gui.AlignFrame.<init>(Unknown Source)
at jalview.io.FileLoader.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
error
What did work (to test if installation was succesfull and Jalview works):
command:
$INSTALL_DIR$/Jalview -nodisplay -open [aln-file] -png [png-file]
result:
Java version: 1.4.2_06
i386 Linux 2.6.9-42.0.10.ELsmp
Jalview Version: 2.2.1
Opening file: [aln-file]
Creating PNG image: [png-file]
I cannot use this last command in the cgi-script (apache user) because I get an error: java.lang.InternalError: Can connect to X11 window server using...
Could you please help me what I should change, why am I getting the java.awt.HeadlessException error?
Thanks. Kind regards,
Paco
--
+----------------------------------------------------------------------+
| Paco Hulpiau, BioIT |
| Bioinformatics Core Facility |
| Department for Molecular Biomedical Research (DMBR) |
| VIB - Ghent University |
| Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium |
| Tel : +32-(0)9-33-13.693 email: paco.hulpiau@dmbr.ugent.be |
| Fax : +32-(0)9-33-13.609 www: http://www.dmbr.ugent.be/bioit |
+----------------------------------------------------------------------+
****** ADDITIONAL INFORMATION ******
Tried to duplicate with a VMware appliance but could not download an appropriate appliance. (blocked by local network environment)
Possible unix+jre+no_X is:http://torrent.vmware.com/torrents/jasapp.rar.torrent
Andrew suggests the dnd initialization is the problem. Workaround in next release would be to disable dnd initialization in headless mode.
Hello
I'm having problems running Jalview on our server.
The following doesn't work (need to use Jalview in cgi-script for a tool with webinterface):
command:
java -Djava.awt.headless=true -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -nodisplay
-open [aln-file] -png [png-file]
result:
Java version: 1.4.2_06
i386 Linux 2.6.9-42.0.10.ELsmp
Jalview Version: 2.2.1
Opening file: [aln-file]
java.awt.HeadlessException
at java.awt.dnd.DropTarget.<init>(Unknown Source)
at java.awt.dnd.DropTarget.<init>(Unknown Source)
at jalview.gui.AlignFrame.init(Unknown Source)
at jalview.gui.AlignFrame.<init>(Unknown Source)
at jalview.gui.AlignFrame.<init>(Unknown Source)
at jalview.io.FileLoader.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
error
What did work (to test if installation was succesfull and Jalview works):
command:
$INSTALL_DIR$/Jalview -nodisplay -open [aln-file] -png [png-file]
result:
Java version: 1.4.2_06
i386 Linux 2.6.9-42.0.10.ELsmp
Jalview Version: 2.2.1
Opening file: [aln-file]
Creating PNG image: [png-file]
I cannot use this last command in the cgi-script (apache user) because I get an error: java.lang.InternalError: Can connect to X11 window server using...
Could you please help me what I should change, why am I getting the java.awt.HeadlessException error?
Thanks. Kind regards,
Paco
--
+----------------------------------------------------------------------+
| Paco Hulpiau, BioIT |
| Bioinformatics Core Facility |
| Department for Molecular Biomedical Research (DMBR) |
| VIB - Ghent University |
| Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium |
| Tel : +32-(0)9-33-13.693 email: paco.hulpiau@dmbr.ugent.be |
| Fax : +32-(0)9-33-13.609 www: http://www.dmbr.ugent.be/bioit |
+----------------------------------------------------------------------+
****** ADDITIONAL INFORMATION ******
Tried to duplicate with a VMware appliance but could not download an appropriate appliance. (blocked by local network environment)
Possible unix+jre+no_X is:http://torrent.vmware.com/torrents/jasapp.rar.torrent
Andrew suggests the dnd initialization is the problem. Workaround in next release would be to disable dnd initialization in headless mode.