• Install GitHub Desktop:
• GitHub for Windows https://windows.github.com/
• GitHub for Mac https://mac.github.com/
• Install a command-line git option for your platform:
• Git: https://git-scm.com/downloads

• Begin by cloning the LabKey server repository from git into a directory such as labkeyHome.

git clone https://github.com/LabKey/server.git labkeyHome

• Clone the following core repositories. Note that the first two go into $LABKEY_HOME\server\modules, while the third goes into $LABKEY_HOME\server.

$LABKEY_HOME\server\modules> git clone https://github.com/LabKey/platform.git

$LABKEY_HOME\server\modules> git clone https://github.com/LabKey/commonAssays.git

$LABKEY_HOME\server> git clone https://github.com/LabKey/testAutomation.git

An abbreviated map of your finished enlistment, showing the main folder structure (with many other elements omitted):

LABKEY_HOME (i.e. C:\dev\labkey\labkeyHome)
│
└───server
    │
    ├───modules
    │   ├───commonAssays
    │   └───platform
    │
    └───testAutomation

• If you will be using a branch other than develop (the default branch when you clone a repository), you can check out all repositories to a given branch, by using the following commands from the root of your enlistment. First recursively check out all the subdirectories, then check out the root on the same branch. For example, to switch from develop to the release21.11-SNAPSHOT branch:

  $LABKEY_HOME> gradlew gitCheckout -Pbranch=release21.11-SNAPSHOT
  $LABKEY_HOME> git checkout release21.11-SNAPSHOT

• You could also choose to check out each repository, including the server repository separately. For example, to change the platform repo to the release21.11-SNAPSHOT branch:

  $LABKEY_HOME\server\modules> cd platform
  $LABKEY_HOME\server\modules\platform> git checkout release21.11-SNAPSHOT

• Download the most recent recommend version of OpenJDK.
• To install the JDK, unzip the archive to a chosen directory (for example, C:\labkey\apps\jdk-##).

• Download the most recent supported release of Tomcat. Note: Download a ZIP or TAR.GZ distribution, not the Windows Service Installer.
• To install Tomcat, unzip it to a chosen directory (for example, C:\labkey\apps\tomcat-#.#.##).

• Install the latest supported version of the PostgreSQL database.
• Take note of the username/password you select during installation.

• Windows:
• Download and run the Windows PostgreSQL one click installer.
• Linux:
• PostgreSQL: Install using your Linux machine's native tools or download a PostgreSQL binary package. Follow the instructions in the downloaded package to install PostgreSQL.

• Create a ".gradle" directory in your home directory.
• On OSX and Linux, typically: /Users/<you>/.gradle.
• On Windows, typically: C:\Users\<you>\.gradle). Note: the Windows file explorer may not allow you to create a folder beginning with a period. To solve this navigate to C:\Users\<you>\ in the command prompt and type mkdir .gradle.
• Create a gradle.properties file in the .gradle directory using the following process:
• Copy the file $LABKEY_HOME/gradle/global_gradle.properties_template to C:\Users\<you>\.gradle. Rename the file to create a file named gradle.properties.
• In the gradle.properties file, substitute your <CATALINA_HOME> directory (the location of your Tomcat installation), including the specific version number, for the value after systemProp.tomcat.home. Use forward slashes, not backslashes, for the Tomcat path, even on Windows. For example:

  systemProp.tomcat.home=C:/labkey/apps/apache-tomcat-#.#.##

• JAVA_HOME
• Create or modify the system environment variable JAVA_HOME so it points to your JDK installation location (for example, C:\labkey\apps\jdk-##). Note: If you've already set the JAVA_HOME variable to point to your installation of the JRE, you should modify it to point to the JDK.
• CATALINA_HOME
• Create or modify the system environment variable CATALINA_HOME so that it points to your Tomcat installation (for example, C:\labkey\apps\tomcat-#.#.##).
• PATH
• Add the JDK to your system PATH. Using the JAVA_HOME variable will simplify upgrades later

  %JAVA_HOME%\bin

• Add the following location to your system PATH. This directory won't exist yet, but add it to the path anyway. The Gradle build downloads binaries used by the server, such as graphvis, dot, and proteomics tools, to this directory.

  $LABKEY_HOME\build\deploy\bin

• For example, C:\dev\labkey\labkeyHome\build\deploy\bin.

• Download and install the latest version of IntelliJ IDEA. Either the Community or Ultimate Edition will work.

• Run the following gradle commands to configure the workspace and other default settings:

gradlew ijWorkspaceSetup
gradlew ijConfigure

• Build the application from the command line

gradlew deployApp

• Open the LabKey project in IntelliJ:
• Launch IntelliJ.
• If your IntelliJ install is brand new, you will see the "Welcome to IntelliJ" pop up screen. Click Open.
• If you have previously installed IntelliJ, select File > Open.
• Select the LabKey IntelliJ project directory: $LABKEY_HOME
• Set Path Variables
• Select File > Settings > Appearance & Behavior > Path Variables. (On a Mac, the menu path is IntelliJ IDEA > Preferences > Appearance & Behavior > Path Variables).
• Click the plus icon in the upper right. Set the CATALINA_HOME path variable to <CATALINA_HOME>, the root directory of your Tomcat installation, for example, C:\labkey\apps\apache\apache-tomcat-#.#.##.
• If developing with TypeScript, add a NODE_PATH variable as well and set it to the path to the node binary that is installed by the build, for example, $LABKEY_HOME\build\.node\node-v#.#.##\bin\node
• Click OK to close the Settings window.
• Configure the Target JDK
• In IntelliJ, select File > Project Structure.
• Under Project Settings, click Project.
• Under Project SDK click New and then click JDK.
• Browse to the path of your JDK, for example, (C:\java\jdk-##), and click OK.
• Click Edit. Change the name of the JDK to "labkey".
• Click OK to close the Project Structure window.
• Open the Gradle tool window at View > Tool Windows > Gradle.

• Click the refresh icon. This will take as much as 5-20 minutes. You should start seeing messages about its progress. If not, something is probably hung up. Wait for this sync to complete before progressing with further IntelliJ configuration steps.

Edit configuration options as follows:

• Select Run > Edit Configurations. (If the menu is greyed-out, wait until IntelliJ finishes indexing the project files.)
• Open the Application node in the left panel and select LabKey Dev.
• The following instructions apply to IntelliJ version 2020.3. You can update now, or for earlier releases of IntelliJ, follow this section in the documentation archives
• From the Modify options... menu, check that both Add VM Options and Use classpath of module are checked.

• Hover over the entry panels in the upper part of the Run panel to see a description of what to select or enter in each one.
• VM options:

• Confirm that the path separators are appropriate for your operating system. On Windows, ensure that the paths to the jar files are separated by semicolons. For example: "./bin/bootstrap.jar;./bin/tomcat-juli.jar;C:/Program Files (x86)/JetBrains/IntelliJ IDEA 20##.#.#/lib/idea_rt.jar". For Macs, the paths should be separated by a colon (:) instead.
• Check that any JVM memory settings (like "-Xms###" and "-Xmx###") in this line are sufficient (if present at all). Determine the correct values in the topic Configure Tomcat Webapp Memory. If these settings are not present, the system allocations for memory will be used.
• To run your instance in development mode include the argument -Ddevmode=true
• For JDK 16 and up, include the arguments --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED
• Select classpath:

• Hover over the upper right panel and set the classpath to "...platform.api.main" (or "api_main" or "org.labkey-api_main" in previous releases).
• Working directory:
• Confirm that this points to your current Tomcat installation (i.e. to the same location as you set CATALINA_HOME).
• Click OK, to close the Run/Debug Configurations window.

• Open the file $LABKEY_HOME/server/configs/pg.properties
• Edit the file, adding your values for the jdbcUser and jdbcPassword. (This password is the one you specified when installing PostgreSQL. If your password contains an ampersand or other special XML characters, you will need to escape them, as the value will be substituted into an XML template without encoding. For example, if your JDBC password is "this&that", then use the escaped version "this&amp;that".)

• In a command window, go to $LABKEY_HOME
• Run "gradlew pickPg" to configure labkey.xml with the corresponding database settings.
• You may need to manually create the directory <CATALINA_HOME>/conf/Catalina/localhost.

• On the command line, go to the $LABKEY_HOME directory, and invoke the gradle build target:

  gradlew deployApp

• Select Run > Debug 'LabKey Dev' in IntelliJ.
• If Tomcat starts up successfully, navigate your browser to http://localhost:8080/labkey to begin debugging (assuming that your local installation of Tomcat is configured to use the Tomcat default port 8080).

• Install and configure the R programming language