1) Download caTissue suite from caTissue site (​https://gforge.nci.nih.gov/frs/?group_id=689) named with caTissue v1.2 installable
2) Once you have downloaded the caTISSUE_SUITE_v12_Installable_Pack.zip, extract the contents of the file to any directory.
This folder contains two additional compressed files; caTissue_Suite_v1.2_Installable and caTissue_Suite_API_Client_v1.2_Installable
3) Unzip the caTissue_Suite_v1.2_Installable.zip, extract the contents of the file to any directory.
4) Unzip the caTissue_Suite_API_Client_v1.2_Installable.zip, extract the contents of the file to any directory.
5) In the installation folder caTissueInstall.properties is the Property file in which all the application configuration parameters are listed, we need to change it according to our local environment
6) In the installation folder build.xml is ANT script used to deploy the application on a JBoss server. This also creates the database schema for Oracle or MySQL.
7) In the installation folder SQL folder containing SQL scripts required for deployment
8) In the installation folder modules folder containing various caTissue modules
9) JBoss version should be 4.2.3 GA and Mysql version should be 5.0.45
10) In order to prevent lower case problem in ubuntu mysql you have to set set lower_case_table_names=1 in your /etc/mysql/my.cnf file.
11) Once above step is done shutdown the mysql server and restart it.
12) Before starting deployment make sure that jboss shouldn't be running.
13) Create the database first (eg: catissuecore) in mysql before starting of the building the application, as shown below,

Drop DATABASE if exists catissuecore;

CREATE DATABASE catissuecore;

GRANT ALL PRIVILEGES ON catissuecore.* TO 'root'@'localhost' IDENTIFIED BY 'root' WITH GRANT OPTION;

GRANT ALL PRIVILEGES ON catissuecore.* TO 'root'@'%' IDENTIFIED BY 'root' WITH GRANT OPTION;

USE mysql;

UPDATE User SET File_priv = 'Y' where User='root';

FLUSH PRIVILEGES;

14) There seems to be a problem with a missing log4j.properties in the root config directory, so create an empty log4j.properties file in jboss-4.2.3.GA/server/default/catissuecore-properties
15) /usr/local/jboss/server/default/lib> mv hibernate3.jar hibernate3.jar.bak
16) /usr/local/jboss/bin> pico run.conf # set the jboss configuration options, MaxPermGen etc as per the catissue deployment guide
17) Start deploying the catissue application using build.xml with the argument deploy_all, if you see any error while in deployment because of upgrade_metadata_cnstrProp.sql then uncomment ALTER TABLE DYEXTN_COLUMN_PROPERTIES TYPE = INNODB; and ALTER TABLE DYEXTN_CONSTRAINTKEY_PROP TYPE = INNODB; in the same file. Start redeploying the application.
18) If you see any errors in building the application, once you resolved the issues freshly build the application with the arguments clean_server and delete_files (delete the previously created dependencies). Once this is done then you build the application with deploy_all.
19) Once build is successful war file will be automatically deployed into your jboss, start the jboss server.
20) Once the JBoss server is started, you can access the application using a web browser. The following is the URL pattern used for the application: ​http://machine_name:port_number/catissuecore.[[BR]] 21) When the browser displays the home page of caTissue Suite, you can log on to the application by specifying the values which were configured in first.admin.emailAddress and first.admin.password of caTissueInstall.properties before deployment.

Following is the sample caTissueInstall.properties file

---

#Enter absolute path of the installed directory of JBoss server {JBOSS_HOME}.
#Please note that the path must be separated by Unix style path separator "/".
jboss.home.dir=/home/localadmin1/jboss-4.2.3.GA

#Please specify the server configuration name of jboss where you want to deploy.
#By default it is set to 'default' configuration. This is useful if someone wants
#to run multiple instances of suite application on same jboss.
jboss.server.name=default

#Enter server port on which JBoss is listing the client request
# Please do not specify the port number in case of an Apache Front ended server
#Default port is 8080
jboss.server.port=8080

#Hostname or IP address of the machine on which the JBoss server is running.
#CAUTION: This parameter should not be set to localhost. Set the actual hostname or IP address
jboss.server.host=localhost

#Enter yes/no to specify Secure HTTP connection
jboss.container.secure=

#database type permissible values: oracle or mysql
database.type=mysql

#Hostname or IP address of the machine on which the database server is running.
database.host=localhost

#Port number to connect with the database server
#Default port for MySQL : 3306
#Default Port for Oracle: 1521
database.port=3306

#Oracle TNS name, applicable only when database.type=oracle
oracle.tns.name=

database.name=catissuecore
database.username=root
database.password=root

#If CAS authentication server needs to be deployed on the
#same server as caTissue (specified by jboss.home.dir), then set this property to "true"
deploy.cas.on.catissue.jboss=true

#If cas.deploy is "false", then fill the following CAS related properties:
#Hostname or IP address of the machine on which the CAS server is running.
#CAUTION: This parameter should not be set to localhost. Set the actual hostname or IP address
cas.jboss.server.host=
cas.jboss.port=
#Enter yes/no to specify Secure HTTP connection for CAS
cas.jboss.container.secure=
#CAS is deployed on HTTPS server then Specify the .keystore file path of CAS server.
cas.server.keystore.path=

email.administrative.emailAddress=
email.sendEmailFrom.emailAddress=
email.mailServer=

# Option to use the common package's email handler on server exception. Values = [true|false]
# Default = [false]
use.email.commonpackage.config=false
# Send the exception email to e-addresses. Can have comma seperated values.
email.sendEmailTo.emailAddress=
# Admin Email address. This would be included in case above entry is empty or invalid.
email.admin.support.emailAddress=
# Email-From Name.
email.sendEmailFrom.name=
# The subject line of the email.
email.exception.subject=System Exception Occured.

#Application login timeout interval in minutes.
#Default value is 30 minutes
session.timeout=30
#sets the addition info on home page
app.additional.info=

#Information related to first administrator account
first.admin.department=d
first.admin.institution=i
first.admin.cancerresearchgroup=c
first.admin.emailAddress=admin@…
first.admin.password=Login123

#Enter path for the MMTx home directory
caties.mmtx.home=

#Values for DE API
caCORE.jBoss.home.dir=
caCORE.project.name=

#Choose below option to associate dynamic extensions default clinical and pathology forms to the Collection Protocols.
#Choose false to show all clinical and pathology default annotations for data entry
#Choose true and edit the Show_Hide_Forms.xml present in the installable folder to associate selective forms to Collection Protocol for data entry
show.hide.forms.based.on.CPs=false

#URL needed for category creation.
Application.url=

#Set the location where caCore is generated
cacore.deployable.location=./cacore_deployable

#Comma separated Entity Groups which are to be excluded.
exclude.entitygroup=

#Comma separated Entity Groups which are only to be included.
include.entitygroup=

#Set the owner for the old saved queries prior to v1.2. Enter the login name of the user whom
#you want to make the owner.
saved.query.owner=

#CSM DATABASE CREDENTIALS
csm.database.type=
csm.database.host=
csm.database.port=
csm.database.name=
csm.database.username=
csm.database.password=