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Welcome to the caNanoLab = 2.4 Installation Guide.
Get Support
For any general information about the=
application, support, or to report a bug, contact caNanoLab-Support@ISB-CGC.org=
a>.
Print the Guide
If you want to print or export content from the guide, refer to Pr=
inting and Exporting to Different Formats.
Topics in this document include:
For more information about the 2.4 updates, refer to the caNanoLab 2.4 Release Note<= /a>.
Download each of the following tools and follow the installation instruc= tions provided with each respective product for your environment. Assistanc= e from a MySQL database administrator is expected to properly configure the= MySQL database. For MySQL database configuration and maintenance, it is al= so helpful to download the MySQL workbench (suite of GUI tools) at the foll= owing page:
http://www.mysql.com/downloads/workbench/ &nb= sp;
Product |
Link |
---|---|
Java Software Development Kit (JDK) version 8= .0 and set JAVA_HOME |
|
Wildfly version 8.2.0.Final |
|
Jakarta Ant version 1.9.x and set ANT_HOME en= vironment variable |
|
MySQL version 5.1.x |
|
Apache Maven 3.3.x or higher |
Downloads for caNanoLab are available at the caNanoLab GitHub Repository= :
https://github.com/CBIIT/cananolab/releases <= /p>
The caNan= oLab Software License applies.
Follow these steps to set the build and deploy properties required for b= uilding and deploying caNanoLab.
Download the following file:
https://github.com/CBIIT/ca= nanolab/archive/refs/tags/2.4.0-qa6.zip
Extract the above file to a location on your local system, for example,&= nbsp;C:\caNanoLab_2.3. and navigate into the =E2=80=9Csoftware=E2=80=9D dir= ectory to reach the source. (This location is referred as <CANANOLA= B_SOURCE> throughout the document). Verify that the following five = folders exist in the directory <CANANOLAB_SOURCE>:
build
cananolab-db
cananolab-grid
cananolab-webapp
common
Edit the Ant properties file, build.properties, at <CANANOL= AB_SOURCE>/build by specifying values for the following properties.=
Property |
Description |
---|---|
file.repository.dir |
A directory on the system that hosts the Wildfly application server for =
storing uploaded files, for example, Writable Directory Create this directory prior to starting the application, and ensure that=
the user who starts the Wildfly server has Write access. If working o=
n Windows platform, use either double back slashes |
admin.email |
The email address that receives requests for = new user accounts, for example, the NCI CBIIT application support email for= the NCI CBIIT installation, for example, NCIAppSupport@nih.gov.= |
ldap.authentication.enabled |
A Boolean flag to indicate whether or not to =
use LDAP for user authentication. caNanoLab 2.1.1 and beyond does not suppo=
rt LDAP authentication. Set this to |
database.server |
The name of the server hosting the database, =
for example, |
database.port |
The database port number, for example, <= code>3306. |
database.user |
The database user name used in the caNanoLab =
application, for example, |
database.password |
The password for the database that the user s=
pecified above, for example, |
database.system.user |
The system database user name with privileges=
to create a database, create tables, and grant user accesses to a database=
, for example, |
database.system.password |
The password for the system database that the=
user specified above, for example, |
jboss.server.dir |
The Wildfly server directory, for exampl= e:
|
https://github.com/CBIIT/cananolab/blob/2.4.0-qa6/softwa= re/cananolab-webapp/db-scripts/2.4.0/db_update_2.4.0.sql
# |
Action |
---|---|
1 |
Set up an environment variable JBOSS_HOME to point to the Wild= fly installation directory. Windows Platform <= /span>
If working on the Windows platform, use either double back slashes
//=
or a single forward slash / as the file separator, for=
example, JBOSS_HOME=3DC:/wildfly-8.2.0.Final (C:\wildfly=
-8.2.0.Final would fail).
|
2 |
Execute the Ant build script build.xml locate= d at <CANANOLAB_SOURCE>/software/cananolab-webapp/build.xml = ;with the target dist. Example: Issue the following com= mands to execute the Ant script:
Successful execution of the Ant scri= pt generates the following artifacts that include two deployable web archiv= e war files, configuration files and libraries for running the web applicat= ion in the Wildfly environment, and also places these artifacts in the appr= opriate directories under <JBOSS_HOME>. Artifacts generated are = also available in the following folder under <CANANOLAB_SOURCE>: = ;
|
3 |
We recommend increasing the JBoss JVM heap si= ze to 2G bytes and permanent generation (permgen) memory space to 256M byte= s by updating the file <JBOSS_HOME>/bin/standalone.conf wit= h the following JAVA_OPTS:
This configuration file is read when Wildf= ly server starts. For a standalone server, pass in the JVM settings e=
ither as command line arguments when executing the |
4 |
Create a new directory structure
Create a new directory structure
|
5 | Start JBoss application server in Standalone = mode. From
The cli script= s 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:
For Linux envi= ronment:
Ru=
n the remaining After suc= cessful completion, the following output appears in the window.
|
Once the deployment artifacts are deployed and the Wildfly application s= erver is correctly configured, shutdown and restart the Wildfly application= server, which in turn starts the caNanoLab application.
Open the URL, http://<APP_SERVER_URL>/caNanoLab/
, for=
example:
http://localhost:8080/caNanoLab
The Welcome/Login page appears.