[EMBOSS] EMBOSS and Jemboss installation problems
Pierre Scotney
pscotney at hotmail.com
Wed Mar 24 04:13:01 UTC 2004
>From: "Dr T. Carver" <tcarver at rfcgr.mrc.ac.uk>
>
>The problem is likely to be that you precompiled emboss before running
>the install script. There is no need, the install script does this for
>you with the correct java flags. Try a 'make clean' and then run the
>install script.
Hi Tim,
I tried make clean and a freshly unpacked source tree but both times when
executing the install-jemboss-server.sh script with the standalone option
there is an error in the build phase:
/bin/sh ../../mkinstalldirs /usr/local/emboss/share/EMBOSS/jemboss/lib
/usr/bin/install -c -m 644 README
/usr/local/emboss/share/EMBOSS/jemboss/lib/README
/usr/bin/install -c -m 644 activation.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/activation.jar
/usr/bin/install -c -m 644 jakarta-regexp-1.2.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar
/usr/bin/install -c -m 644 mail.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/mail.jar
/usr/bin/install -c -m 644 xerces.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/xerces.jar
/usr/bin/install -c -m 644 jalview.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/jalview.jar
/usr/bin/install -c -m 644 jcert.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/jcert.jar
/usr/bin/install -c -m 644 jnet.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/jnet.jar
/usr/bin/install -c -m 644 jsse.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/jsse.jar
/usr/bin/install -c -m 644 JembossPrintAlignment.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/JembossPrintAlignment.jar
/usr/bin/install -c -m 644 grout.jar
/usr/local/emboss/share/EMBOSS/jemboss/lib/grout.jar
make[4]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
make[3]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
make[2]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
Making install in org
make[2]: Entering directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org'
Making install in emboss
make[3]: Entering directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss'
Making install in jemboss
make[4]: Entering directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss'
Making install in editor
make[5]: Entering directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[6]: Entering directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make install-exec-hook
make[7]: Entering directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/editor
/usr/bin/install: cannot stat `*.class': No such file or directory
make[7]: *** [install-exec-hook] Error 1
make[7]: Leaving directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[6]: *** [install-exec-am] Error 2
make[6]: Leaving directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[5]: *** [install-am] Error 2
make[5]: Leaving directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss'
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss'
make: *** [install-recursive] Error 1
--------------------------------------------------------------
EMBASSY packages can optionally be installed along with
the EMBOSS applications, see:
http://www.uk.embnet.org/Software/EMBOSS/EMBASSY/
--------------------------------------------------------------
Install EMBASSY packages (y,n) [y]?
n
-------------------------- ClustalW --------------------------
To use emma (EMBOSS interface to ClustalW) Jemboss needs to
know the path to the clustalw binary.
Enter the path to clustalw or press return to set
this later in jemboss.properties
-------------------------- Primer3 --------------------------
To use eprimer3 (EMBOSS interface primer3 from the Whitehead
Institute) Jemboss needs to know the path to the primer3_core
binary.
Enter the path to primer3_core or press return to set
this later in jemboss.properties
java.io.FileNotFoundException:
/usr/local/emboss/share/EMBOSS/jemboss/resources/wossname.jar (No such file
or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
at sun.tools.jar.Main.run(Main.java:134)
at sun.tools.jar.Main.main(Main.java:904)
java.io.FileNotFoundException:
/usr/local/emboss/share/EMBOSS/jemboss/resources/resources.jar (No such file
or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
at sun.tools.jar.Main.run(Main.java:134)
at sun.tools.jar.Main.main(Main.java:904)
error: cannot read:
/usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java
1 error
error: cannot read:
/usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java
1 error
mv: cannot stat
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No
such file or directory
touch: creating
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No
such file or directory
./install-jemboss-server.sh: line 362:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 366:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 367:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 370:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 374:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 375:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 381:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 382:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 383:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 384:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 388:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
./install-jemboss-server.sh: line 389:
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such
file or directory
cp: cannot stat
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No
such file or directory
Changed /usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties
to reflect this installation (original in jemboss.properties.orig)
sed: can't read /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh: No
such file or directory
mv: cannot stat `/usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh': No
such file or directory
To run Jemboss:
cd /usr/local/emboss/share/EMBOSS/jemboss
./runJemboss.sh
lt looks like the editor classes are not being built:
$ ls -R -w 80 jemboss/
jemboss/:
editor JembossJarUtil.class JembossParams.java parser
FileManager.java JembossJarUtil.java Jemboss$winExit.class programs
gui Jemboss.java Makefile server
Jemboss$1.class JembossLogo.java Makefile.am soap
Jemboss.class JembossParams.class Makefile.in
jemboss/editor:
AlignApplet.java Makefile
AlignJFrame.java Makefile.am
ColourJFrame.java Makefile.in
ColourMenu.java Matrix.java
ColourPanel.java MatrixJFrame.java
Consensus.java PatternJFrame.java
ConsensusOptions.java PlotConsensus.java
GraphicSequenceCollection.java PrettyPlotJFrame.java
GroutAlignJFrameEvent.java PrintableJTable.java
GroutAlignJFrame.java PrintAlignmentImage.java
GroutAlignJFrameListener.java PrintAlignment.java
GroutGraphicSequenceCollectionEvent.java Sequence.java
GroutGraphicSequenceCollection.java SequenceJPanel.java
GroutGraphicSequenceCollectionListener.java SequenceNameJButton.java
GroutSequence.java SequenceProperties.java
GroutSequenceJPanel.java SequenceReader.java
IDTableJFrame.java SequenceSaver.java
jemboss/gui:
AdvancedOptions$1.class Makefile SetUpMenuBar$10.class
AdvancedOptions$2.class Makefile.am SetUpMenuBar$11.class
AdvancedOptions.class Makefile.in SetUpMenuBar$1.class
AdvancedOptions.java MemoryComboBox.class SetUpMenuBar$2.class
Browser.java MemoryComboBox.java SetUpMenuBar$3.class
BuildProgramMenu$1.class ResultsMenuBar.java SetUpMenuBar$4.class
BuildProgramMenu$2.class ScrollPanel.class SetUpMenuBar$5.class
BuildProgramMenu$3.class ScrollPanel.java SetUpMenuBar$6.class
BuildProgramMenu$4.class sequenceChooser SetUpMenuBar$7.class
BuildProgramMenu$5.class SequenceData.class SetUpMenuBar$8.class
BuildProgramMenu$6.class SequenceData.java SetUpMenuBar$9.class
BuildProgramMenu$7.class SequenceList$1.class SetUpMenuBar.class
BuildProgramMenu$8.class SequenceList$2.class SetUpMenuBar.java
BuildProgramMenu.class SequenceList$3.class ShowResultSet.java
BuildProgramMenu.java SequenceList$4.class ShowSavedResults.java
ColumnData.class SequenceList$5.class SplashThread.class
DragJTable.class SequenceList$6.class SplashThread.java
filetree SequenceList$7.class startup
form SequenceList.class SwingWorker.java
ImageIconJPanel.java SequenceList.java
LaunchJalView.java SequenceListTableModel.class
jemboss/gui/filetree:
DragTree$1.class LocalAndRemoteFileTreeFrame$1.class
DragTree$2.class LocalAndRemoteFileTreeFrame$2.class
DragTree$3.class LocalAndRemoteFileTreeFrame$3.class
DragTree$4.class LocalAndRemoteFileTreeFrame$4.class
DragTree$5.class LocalAndRemoteFileTreeFrame$5.class
DragTree.class LocalAndRemoteFileTreeFrame.class
DragTree.java LocalAndRemoteFileTreeFrame.java
DragTree$PopupListener.class Makefile
FileEditorDisplay.java Makefile.am
FileNode$1.class Makefile.in
FileNode.class RemoteDragTree.java
FileNode.java RemoteFileNode.java
FileSave.java RemoteFileTreePanel.java
FileSaving.java
jemboss/gui/form:
AlignFormat.java Makefile.am SetInFileCard.java
ApplicationNamePanel.java Makefile.in SetOutFileCard.java
BuildJembossForm.java MultiLineToolTipUI.java TextFieldFloat.java
JembossComboPopup.java PlafMacros.java TextFieldInt.java
LabelTextBox.java ReportFormat.java TextFieldSink.java
ListFilePanel.java SectionPanel.java
Makefile Separator.java
jemboss/gui/sequenceChooser:
CutNPasteTextArea.java Makefile OutputSequenceAttributes.java
FileChooser.java Makefile.am SequenceFilter.java
InputSequenceAttributes.java Makefile.in TextAreaSink.java
jemboss/gui/startup:
Database.java Makefile Makefile.am Makefile.in ProgList.java
jemboss/parser:
acd AcdVarResolve.java AjaxUtil.java Makefile.am
AcdFunResolve.java Ajax.class Dependent.java Makefile.in
AcdVariableResolve.java Ajax.java Makefile ParseAcd.java
jemboss/parser/acd:
ApplicationFields.java Makefile Makefile.in
ApplicationParam.java Makefile.am
jemboss/programs:
BatchUpdateTimer.java ResultList.java
JembossProcess.class ResultsUpdateTimer.java
JembossProcess.java RunEmbossApplication2.class
ListFile.java RunEmbossApplication2.java
Makefile RunEmbossApplication2$StderrHandler.class
Makefile.am RunEmbossApplication2$StdoutHandler.class
Makefile.in RunEmbossApplication.java
jemboss/server:
AppendToLogFileThread.java JembossServer$3.class JembossThread.java
JembossAuthServer.java JembossServer$4.class Makefile
JembossFileAuthServer.java JembossServer$5.class Makefile.am
JembossFileServer.java JembossServer.class Makefile.in
JembossServer$1.class JembossServer.java TestPrivateServer.java
JembossServer$2.class JembossThread.class TestPublicServer.java
jemboss/soap:
AuthPopup$1.class GetACD.java PendingResults$2.class
AuthPopup$2.class GetHelp.java PendingResults.class
AuthPopup$3.class GetWossname.java PendingResults.java
AuthPopup$4.class JembossRun.java PrivateRequest.java
AuthPopup$5.class JembossSoapException.class PublicRequest.java
AuthPopup$6.class JembossSoapException.java ServerSetup$1.class
AuthPopup.class Makefile ServerSetup$2.class
AuthPopup.java Makefile.am ServerSetup$3.class
CallAjax.java Makefile.in ServerSetup.class
FileList.java MakeFileSafe.java ServerSetup.java
FileRoots.java PendingResults$1.class ShowDB.java
Any ideas of what is going wrong? Is the j2sdk1.3.1 the wrong version to
use?
Regards
Pierre
--
Dr Pierre Scotney
Melbourne
Australia
_________________________________________________________________
Personalise your mobile chart ringtones and polyphonics. Go to
http://ringtones.com.au/ninemsn/control?page=/ninemsn/main.jsp
More information about the EMBOSS
mailing list