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caNanoLab Installation Guide
caNanoLab Installation Guide
Welcome to the caNanoLab 2.4 Installation Guide.

Info
titleGet Support

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For any general information about the application, application support, or to report a bug, contact Application Support (NCIAppSupport@nih.gov).


Print the Guide
If you want to print or export content from the guide, refer to Printing and Exporting to Different Formats.

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For more information about the 2.4 updates, refer to the caNanoLab 2.4 Release Note.   

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Open Source Technologies

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http://www.mysql.com/downloads/workbench/ 

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Product

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Java Software Development Kit (JDK) version 8.0 and set JAVA_HOME 

http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

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Wildfly version 8.2.0.Final

http://wildfly.org/downloads/

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Jakarta Ant version 1.9.x and set ANT_HOME environment variable

http://archive.apache.org/dist/ant/binaries/ 

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MySQL version 5.1.x

http://dev.mysql.com/downloads/mysql/5.1.html

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Apache Maven 3.3.x or higher

https://archive.apache.org/dist/maven/maven-3

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Obtaining the caNanoLab Source Code

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Follow these steps to set the build and deploy properties required for building and deploying caNanoLab.

Step 1.   Extract caNanoLab

Download the following file:

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Step 1. To migrate from caNanoLab 2.3 to caNanoLab 2.4 

a   a Execute the following script:

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Step 2. caNanoLab installation instructions to upgrade to 2.3

a  Follow Follow these steps to deploy the caNanoLab application.

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Action

1

Set up an environment variable JBOSS_HOME to point to the Wildfly installation directory.

Info
titleWindows Platform
If working on the Windows platform, use either double back slashes // or a single forward slash / as the file separator, for example, JBOSS_HOME=C:/wildfly-8.2.0.Final (C:\wildfly-8.2.0.Final would fail).

2

Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/software/cananolab-webapp/build.xml with the target dist.

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.3\software\cananolab-webapp
C:\caNanoLab_2.3\software\cananolab-webapp>ant dist 

Successful execution of the Ant script generates the following artifacts that include two deployable web archive war files, configuration files and libraries for running the web application in the Wildfly environment, and also places these artifacts in the appropriate directories under <JBOSS_HOME>. Artifacts generated are also available in the following folder under <CANANOLAB_SOURCE>: 

target/dist/cananolab-webapp/caNanoLab.war 
target/dist/common/ApplicationSecurityConfig.xml 
target/dist/common/mysql-connector-java-5.1.26.jar 
target/dist/common/properties-service.xml
target/dist/common/bcprov-jdk15on-1.69.jar 
target/dist/common/caNanoLab_modules.cli 
target/dist/common/caNanoLab_setup.cli 
target/dist/common/caNanoLab_deploy.cli

target/dist/common/wikihelp.properties

3

We recommend increasing the JBoss JVM heap size to 2G bytes and permanent generation (permgen) memory space to 256M bytes by updating the file <JBOSS_HOME>/bin/standalone.conf with the following JAVA_OPTS:

JAVA_OPTS="-Xms512m -Xmx2048m -XX:PermSize=128m 
-XX:MaxPermSize=256m -Dsun.rmi.dgc.client.gcInterval=3600000
-Dsun.rmi.dgc.server.gcInterval=3600000"

This configuration file is read when Wildfly server starts.

For a standalone server, pass in the JVM settings either as command line arguments when executing the $JBOSS_HOME/bin/standalone.sh script, or by declaring them in $JBOSS_HOME/bin/standalone.conf.
(For Windows users, the script to execute is %JBOSS_HOME%/bin/standalone.bat while the JVM settings can be declared in
%JBOSS_HOME%/bin/standalone.conf.bat.)

4

Create a new directory structure C:/local/content/caNanoLab/artifacts and move the following artifacts.

  • caNanoLab.war
  • bcprov-jdk15on-1.69.jar
  • mysql-connector-java-5.1.26.jar
  • caNanoLab_modules.cli
  • caNanoLab_setup.cli
  • caNanoLab_deploy.cli 

Create a new directory structure C:/local/content/caNanoLab/config and move the following artifacts.

  • ApplicationSecurityConfig.xml
  • wikihelp.properties
5

Start JBoss application server in Standalone mode.

From <install-dir>/bin:

./standalone.sh --server-config=standalone-full.xml

The cli scripts assumes the CLI port is running at 19990. If it is different, update the port number at the second line in the script. 

For Windows environment:

jboss-cli.bat --file=C:/local/content/caNanoLab/artifacts/caNanoLab_modules.cli and press <ENTER>. 

For Linux environment:

jboss-cli.sh --file= /local/content/caNanoLab/artifacts/caNanoLab_modules.cli and press <ENTER>.

Run the remaining caNanoLab_setup.cli and caNanoLab_deploy.cli that deploys the caNanoLab.

After successful completion, the following output appears in the window.

{"outcome"=> "success"}
{"outcome"=> "success"}
{"outcome"=> "success"}
{"outcome"=> "success"}
{
"outcome"=> "success",
"result"=> undefined
}

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c  Restart Restart the application server after the above step to migrate data is completed.

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