[EMBOSS] Installation help

Jeremy Mann jeremy at biochem.uthscsa.edu
Wed May 25 18:31:12 UTC 2005 

Tim Carver said:
> Hi Jeremy
>
> If tomcat is not using 8443 then the deployment of the Jemboss services
> will fail. When you run the script you are asked to cut and paste lines
> into conf/server.xml. Did you do this? Are there any error in the tomcat
> logs/catalina.out.
>
> Btw, running the script from scratch will mean that you need a fresh copy
> of tomcat, EMBOSS and axis and you will need to remove the previous EMBOSS
> installation directories.

I just tried again for the 6th time. Yes, I copy pasted the lines to the
bottom of server.xml.

Catalina.out:

Created MBeanServer with ID: 147c5fc:104151818da:-8000:bcf:1
May 25, 2005 1:23:18 PM org.apache.tomcat.util.digester.Digester fatalError
SEVERE: Parse Fatal Error at line 380 column 6: The markup in the document
following the root element must be well-formed.
org.xml.sax.SAXParseException: The markup in the document following the
root element must be well-formed.
        at
org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown
Source)
        at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown
Source)
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown
Source)
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown
Source)
        at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
        at
org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown
Source)
        at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561)
        at org.apache.catalina.startup.Catalina.load(Catalina.java:473)
        at org.apache.catalina.startup.Catalina.load(Catalina.java:509)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:324)
        at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:243)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:408)
May 25, 2005 1:23:18 PM org.apache.catalina.startup.Catalina load
WARNING: Catalina.start using conf/server.xml:
org.xml.sax.SAXParseException: The markup in the document following the
root element must be well-formed.
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561)
        at org.apache.catalina.startup.Catalina.load(Catalina.java:473)
        at org.apache.catalina.startup.Catalina.load(Catalina.java:509)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:324)
        at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:243)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:408)
May 25, 2005 1:23:18 PM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/5.5.9
May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardHost start
INFO: XML validation disabled
- Unable to find config file.  Creating new servlet engine config file:
/WEB-INF/server-config.wsdd
May 25, 2005 1:23:21 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
May 25, 2005 1:23:21 PM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
May 25, 2005 1:23:21 PM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/31  config=null
May 25, 2005 1:23:21 PM org.apache.catalina.storeconfig.StoreLoader load
INFO: Find registry server-registry.xml at classpath resource
May 25, 2005 1:23:21 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3219 ms

Install script:
Please wait, starting tomcat.......
Using CATALINA_BASE:   /usr/local/jakarta-tomcat-5.5.9
Using CATALINA_HOME:   /usr/local/jakarta-tomcat-5.5.9
Using CATALINA_TMPDIR: /usr/local/jakarta-tomcat-5.5.9/temp
Using JRE_HOME:       /usr/lib/java/jre


May 25, 2005 1:19:08 PM org.apache.axis.utils.JavaUtils isAttachmentSupported
WARNING: Unable to find required classes (javax.activation.DataHandler and
javax.mail.internet.MimeMultipart). Attachment support is disabled.
Processing file JembossServer.wsdd
Exception: AxisFault
 faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
 faultSubcode:
 faultString: java.net.ConnectException: Connection refused
 faultActor:
 faultNode:
 faultDetail:
        {http://xml.apache.org/axis/}stackTrace:java.net.ConnectException:
Connection refused
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:305)
        at
java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:171)
        at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:158)
        at java.net.Socket.connect(Socket.java:452)
        at com.sun.net.ssl.internal.ssl.SSLSocketImpl.connect(DashoA12275)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.<init>(DashoA12275)
        at
com.sun.net.ssl.internal.ssl.SSLSocketFactoryImpl.createSocket(DashoA12275)
        at
org.apache.axis.components.net.JSSESocketFactory.create(JSSESocketFactory.java:92)
        at
org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:130)
        at
org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:382)
        at
org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:88)
        at
org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
        at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
        at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
        at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147)
        at org.apache.axis.client.Call.invokeEngine(Call.java:2737)
        at org.apache.axis.client.Call.invoke(Call.java:2720)
        at org.apache.axis.client.Call.invoke(Call.java:1756)
        at org.apache.axis.client.AdminClient.process(AdminClient.java:438)
        at org.apache.axis.client.AdminClient.process(AdminClient.java:403)
        at org.apache.axis.client.AdminClient.process(AdminClient.java:409)
        at org.apache.axis.client.AdminClient.process(AdminClient.java:319)
        at org.apache.axis.client.AdminClient.main(AdminClient.java:462)

        {http://xml.apache.org/axis/}hostname:bcf





-- 
Jeremy Mann
jeremy at biochem.uthscsa.edu

University of Texas Health Science Center
Bioinformatics Core Facility
http://www.bioinformatics.uthscsa.edu
Phone: (210) 567-2672

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