installing SOAPLAB2+EMBOSS problem!!

[xiangwulu]

Hi all,

i tried to install soaplab2+emboss on amazon web service instance,

i got java, ant, maven, tomcat installed, built soaplab2 firstly, it can be accessed at:http://ec2-176-34-220-249.eu-west-1.compute.amazonaws.com:8080/soaplab2/,

and then i install emboss followed this site: http://soaplab.sourceforge.net/soaplab2/EmbossNotes.html

but for the step "ant genemboss", i got such error message:


[acd2xml] Processing digest...
[acd2xml] using /root/soaplab2/EMBOSS-6.5.7/share/EMBOSS/acd/digest.acd
[acd2xml] ERROR: Modification of non-creatable array value attempted, subscript -1 at acd.y line 575.
[acd2xml]

BUILD FAILED
/root/soaplab2/soaplab2/xmls/emboss.xml:75: The following error occurred while executing this line:
/root/soaplab2/soaplab2/xmls/acd2xml.xml:58: exec returned: 1

i searched on the internet for the similar error message but not much information useful.

would anyone help? thanks so much!!

[xiangwulu]

probably i should state my problems bit more clear:
i am trying to install soaplab2 + emboss on amazon web service.


I used the installation instruction from:
http://soaplab.sourceforge.net/soaplab2/BuildGuide.html soaplab2 installation

http://soaplab.sourceforge.net/soaplab2/EmbossNotes.html emboss installation

I installed java jdk, tomcat, ant, soaplab and emboss on the cloud instance.

The emboss commands worked on the local terminal window ( wossname), but not the server(-bash: wossname: command not found)

here is the my public server address:
http://ec2-176-34-220-249.eu-west-1.compute.amazonaws.com:8080/soaplab2/

this is the error message returned after I run "ant genemboss" command, and i get this error both when i set up soaplab+emboss on local PC and cloud instance:

[acd2xml] Processing digest...
[acd2xml] using /root/soaplab2/EMBOSS-6.5.7/share/EMBOSS/acd/digest.acd
[acd2xml] ERROR: Modification of non-creatable array value attempted, subscript -1 at acd.y line 575.
[acd2xml]


BUILD FAILED
/root/soaplab2/soaplab2/xmls/emboss.xml:75: The following error occurred while executing this line:
/root/soaplab2/soaplab2/xmls/acd2xml.xml:58: exec returned: 1

acd2xml.xml line 58 is: <exec executable="perl" taskname="acd2xml" failonerror="true">


here are my build.properties file:


# If you want to specify some local properties that will be used by
# Ant tasks, copy this file into 'build.properties' and edit it as you
# need.
#
# $Id: build.properties.template,v 1.16 2009/06/26 09:56:00 mahmutuludag Exp $
# --------------------------------------------------------------------
# --------------------------------------------------------------------
# Pointer to your own templates of Soaplab configuration files
# --------------------------------------------------------------------
my.soaplab.properties = testing.soaplab.properties
#my.soaplab.client.properties = testing.soaplab.client.properties
#my.log4j.properties = testing.log4j.properties
# --------------------------------------------------------------------
# Full path to your Tomcat installation.
# --------------------------------------------------------------------
tomcat.home=/etc/tomcat6
# --- Where is your Tomcat listening
tomcat.port = 8080
tomcat.host = ec2-176.34.220.249.eu-west-1.compute.amazonaws.com
# --- For using Tomcat manager to deploy
#tomcat.manager.username = tomcat
#tomcat.manager.password = tomcat
#tomcat.manager.url= http://my.tomcathost:9800/manager
# --------------------------------------------------------------------
# For deploying services to Tomcat
# --------------------------------------------------------------------
# To use metadata (etc.) from other directories than the ones "embedded"
# in the Tomcat webapps structure:

#server.metadata.dir = /root/soaplab2/soaplab2/metadata/generated
#server.runtime.dir = /root/soaplab2/soaplab2/_R_
#server.scripts.dir = /root/soaplab2/run
catalina.base=/var/lib/tomcat6
# --------------------------------------------------------------------
# These properties are for those who wish to use their own, additional
# classes, for the Soaplab2 services. If you write a Soaplab2 plugin,
# these properties are for you.
#
# The classes you wish to add must be packed, usually as jars. The
# directory with the jar files is given by the property
# user.lib.dir. Additionally, a pattern which jars to use can be
# specified by the property user.lib.include.
# --------------------------------------------------------------------
#user.lib.dir =
#user.lib.include = *.jar
# --------------------------------------------------------------------
# Configuring Spinet web client
# --------------------------------------------------------------------
#soaplab.docs.url = http://localhost/~senger/soaplab2/
#local.contact = &lt;a href=&quot;mailto:martin.senger&#64;gmail.com&quot;&gt;Martin Senger&lt;/a&gt;
spinet.welcome.msg = Soaplab at CIT
# --------------------------------------------------------------------
# Specifically for those who are using EMBOSS
# --------------------------------------------------------------------
emboss.home = /root/soaplab2/EMBOSS-6.5.7
emboss.supplier = CIT
emboss.version = 6.5.7
# --------------------------------------------------------------------
# Set how to compile Java source to Java classes
# --------------------------------------------------------------------
#compile.verbose = false
#compile.deprecation = false
#compile.optimize = false
#compile.warnings = true
# -----------------------------------------------------------------------------------------
# For those who prefers additional WSDL files with strongly typed input/output descriptions
# -----------------------------------------------------------------------------------------
#typedinterface.enable = true
================================================== ==


Thanks!!

[xiangwulu]

the above issues is the error i saw the most times. i deleted digest.acd and then it built ok. but i didn't know the reason of this, i didn't change this file after downloaded and unpacked.

this is my aws server address:
http://ec2-176-34-220-249.eu-west-1.compute.amazonaws.com:8080/soaplab2

i run the ant genemboss successful, and in soaplab2 directory run
ant jaxdeploy to deploy the emboss services(edited the config file), but this spinet page still didn't show emboss web services(like the one show here: http://soaplab.sourceforge.net/soaplab2/SpinetClient.html).

has anyone came cross the similar problem? any help is appreciated.