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Directory Set Up

Create the directory structure:

C:
labkey
apps
labkey

Download

Download the following components

Java

Unzip and deploy as follows:

labkey
apps
jdk-12.0.2
  • Set JAVA_HOME environmental variable to C:\labkey\apps\jdk-12.0.2
  • Add %JAVA_HOME%\bin to the PATH

Tomcat

Unzip and deploy as follows:

labkey
apps
jdk-12.0.2
tomcat-9.0.26

Set the environment variable CATALINA_HOME to C:\labkey\apps\tomcat-9.0.26

Install tomcat as a service by running the script distributed with Tomcat:

C:\labkey\apps\tomcat-9.0.26\bin\service.bat install
  • Open the Services panel. Right-click Apache Tomcat 9.0 Tomcat9 and select Properties.
  • In the popup dialog, click the tab Log On. Select Local System account. Click OK.
  • On the Service panel, start Tomcat.
  • Confirm the Tomcat install, by visting the URL:

PostgreSQL

Create the directory C:\labkey\apps\pg-11.5 as below:

labkey
apps
jdk-12.0.2
tomcat-9.0.26
pg-11.5
  • Run the installer .EXE file.
  • Install postgres into the directory above.
  • Save the username and password for later configuration steps.

LabKey Server

  • Unzip LabKey19.1.8-64035.14-community-bin.zip
  • The zip file contains:
    • bin: Binary files required by LabKey Server (only in Windows distributions).
    • labkeywebapp: The LabKey Server web application.
    • modules: LabKey Server modules.
    • pipeline-lib: Jars for the data processing pipeline.
    • tomcat-lib: Required server library jars.
    • labkey.xml: LabKey Server configuration file.
    • manual-upgrade.sh: For use with existing installations.
    • README.txt: A file pointing you to this documentation.
    • VERSION: A file containing the release number and build number.

Main LabKey Binaries and Libraries

  • Copy the following directories:
    • bin
    • labkeywebapp
    • modules
    • pipeline-lib
  • into LABKEY_HOME:
C:\labkey\labkey

Tomcat Libraries

  • Go to the tomcat-lib dir in the distribution:
\LabKey19.1.8-64035.14-community-bin\tomcat-lib
  • Copy the contents of tomcat-lib, these six .jar files:
javax.activation.jar
jtds.jar
labkeyBootstrap.jar
mail.jar
mysql.jar
postgresql.jar
  • into CATALINA_HOME\lib:
C:\labkey\apps\apache-tomcat-9.0.26\lib

Main Configuration File: labkey.xml

  • Create the directory path
C:\labkey\apps\apache-tomcat-9.0.26\conf\Catalina\localhost
  • Copy the file labkey.xml. Find it in the unzipped distribution, and copy this file into the dir path just created, as follows:
C:\labkey\apps\apache-tomcat-9.0.26\conf\Catalina\localhost\labkey.xml

docbase, user, and password

  • In labkey.xml, substitute the values for @@...@@ tokens as below:
    • @@appDocBase@@ - replace with C:\labkey\labkey\labkeywebapp
    • @@jdbcUser@@ - postgres
    • @@jdbcPassword@@ - sa

Start LabKey Server

  • On the Services panel, restart Apache Tomcat
  • If you are installing on a local machine, visit the LabKey home page at:

or, if you are installing on a remote server:

  • For a new server, you are invited to create the initial user profile, which is a Site Administrator.

Windows Install Part 2: Configure the LabKey Web Application

Discussion

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