A record of my personal attempt to install a LabKe(()y development environment in Windows 10 (March 8-9, 2016). Also working on converting the LabKey Excel checklist to markdown.

labkey-windows-install.md

LabKey Development Environment in Windows

https://www.labkey.org/home/Documentation/wiki-page.view?name=svn https://www.labkey.org/home/Documentation/wiki-page.view?name=build

Obtain the LabKey Source Files

• Install Git
• Install IntelliJ Community Edition
• Install TortoiseSVN
• Install R-Studio
• Check Out LabKey source Files Using TortoiseSVN
  • Source: https://hedgehog.fhcrc.org/tor/stedi/trunk
  • Dedstination c:\labkey
  • User: cpas
  • Pwd: cpas
• Install Modules
  • Create LabKey/optionalModules
  • Clone modules into LabKey/optionalModules - All OHSU Comp Bio modules: https://github.com/ohsu-computational-biology - Only current one (03/09/2016): https://github.com/ohsu-computational-biology/bcc - Install Java, Tomcat, and a Database

---

• Install Java SDK (currently V.8)

• Install Tomcat HTTP Server (currently V.9)

  • Instructions: https://tomcat.apache.org/tomcat-8.0-doc/windows-service-howto.html
  • Download "Service" installer
  • Set CATALINA_HOME environment variable to top-level apache tomcat (e.g. C:\Program Files\Apache Software Foundation\Tomcat 7.0)
  • Test: cd %CATALINA_HOME%\bin Tomcat7.exe start
  • Point browser to localhost:8080

• Install PostgreSQL

  Instructions

  • Download and run the Windows PostgreSQL one click installer.
  • Install PostgreSQL as a Windows Service.
  • Keep track of the PostgreSQL Windows Service account name and password. LabKey Server doesn't really care what this password is set to, but we need to ask for it so that we can pass it along to the PostgreSQL installer.
  • Keep track of the database superuser name and password. You'll need these to configure LabKey Server. LabKey Server uses this password to authenticate itself to PostgreSQL.
  • Select the PL/pgsql procedural language for installation when prompted by the installer.
  • We recommend that you install the graphical tool pgAdminIII for easy database administration. Leave the default settings as they are on the "Installation Options" page to include pgAdminIII. If you have chosen to install pgAdminIII, enable the Adminpack contrib module when prompted by the installer.

  Please read the notes below to forestall any difficulties with the PostgreSQL installation

  • You can only install one instance of PostgreSQL on your computer. If you already have PostgreSQL installed, LabKey Server can use that installed instance, provided the version is supported.
  • You may need to disable your antivirus or firewall software before installing PostgreSQL, as the PostgreSQL installer conflicts with some antivirus or firewall software programs. [See for more information] (http://wiki.postgresql.org/wiki/Running_%26_Installing_PostgreSQL_On_Native_Windows).
  • On Windows you may need to remove references to Cygwin from your Windows system path before installing PostgreSQL. See for more information.
  • If you uninstall and reinstall PostgreSQL, you may need to manually delete the data directory in order to reinstall. Bydefault the data directory on a Windows computer is C:\Program Files\PostgreSQL\8.x\data.
  • On Vista, you may need to run 'cmd.exe' as administrator and run the installer .msi from the command line. (But if you are running Vista, you have bigger problems than that.)
  • See also: Notes on Installing PostgreSQL on All Platforms
  • After installation, you may find it helpful to tune PostgreSQL for performance.
  • LabKey guide: https://www.labkey.org/wiki/home/Documentation/page.view?name=installPostgreSQLWindows

Set Environment Variables

• [?] <LABKEY_HOME>/external/ant/bin
• [?] <LABKEY_HOME>/build/deploy/bin DOESN'T EXIST IN MY INSTALLATION
• JAVA_HOME
• CATALINA_HOME (e.g. C:\Program Files\Apache Software Foundation\Tomcat 7.0)
• LABKEY_ROOT (e.g. C:\LabKey)
• [?] LABKEY_GWT_USER_OVERRIDE ?????
• Add to PATH %LABKEY_ROOT%/external/ant/bin;%LABKEY_ROOT%/build/deploy/bin (%LABKEY_ROOT%/build/deploy/bin does not exist)
• ???? Something is wrong here. What is the difference between LABKEY_HOME and LABKEY_ROOT?

Build and Run

• Copy the file <LABKEY_HOME>/server/.idea/workspace.template.xml to create a new file called <LABKEY_HOME>/server/.idea/workspace.xml (This file configures the debug information for LabKey project. To review the debug settings go to Run > Edit Configurations in IntelliJ.)
• Launch IntelliJ Bug Ran into bug here opeining IntelliJ. Can't find java library properly. Submitted to forum/issue https://www.labkey.org/announcements/home/Server/Forum/thread.view?rowId=12579
• In IntelliJ, select File > Open. Select the LabKey IntelliJ project directory, <LABKEY_HOME>/server
• Set the CATALINA_HOME path variable to the root directory of your Tomcat installation, for example, (C:\apache\apache-tomcat-8.0.28). (If IntelliJ doesn't ask for this path, go to File > Settings > Build, Execution, Deployment > Path Variables.)
• Select Run > Edit Configurations. Set Use classpath of module to LabKey using the dropdown.

http://www.itdaan.com/blog/2015/09/17/684456.html

a non fatal error occured during cluster initialisation

https://ohsu.app.box.com/notes/40503308805?s=vjlr081srr9hzlw2tzl07llarvlk05nv

https://www.labkey.org/home/Documentation/wiki-page.view?name=svn

https://www.labkey.org/home/Documentation/wiki-page.view?name=build

https://www.labkey.org/wiki/home/Documentation/page.view?name=postgreSQLInstallNotes

https://wiki.postgresql.org/wiki/Tuning_Your_PostgreSQL_Server

https://www.labkey.org/wiki/home/Documentation/page.view?name=tutorials

https://www.java.com/en/download/help/path.xml

https://www.labkey.org/wiki/home/Documentation/page.view?name=tutorials

https://ohsu.app.box.com/notes/40503308805?s=vjlr081srr9hzlw2tzl07llarvlk05nv

https://www.labkey.org/home/Documentation/wiki-page.view?name=build

z-installation-checklist.md

- [ ] Install a subversion distribution appropriate for your operating system
- [ ] Checkout (download) the LabKey source files

• Install and Configure Required Prerequisites

  • Install the Oracle JDK
  • Install Tomcat 7
  • Enable unicode support for tomcat
  • Install your RDMS
  • Configure Environment Variables and System Path

• Install and Configure IntelliJ IDEA N

  • Open and configure the LabKey Project in IntelliJ N
  • Configure the Target JDK N
  • Configure LabKey Development / Debug Configuration N

Build LabKey Server N Configure the appropriate .properties file N Select the database via 'ant pick_pg' or 'ant pick_mssql' N Build LabKey server via 'ant build' N

Start LabKey Server N

Post Installation Steps N Install and Configure R for Use with LabKey Server N Run the Basic Test Suite N The basic test suite may be run via 'ant drt'

References Setup a Development Machine https://www.labkey.org/wiki/home/Documentation/page.view?name=build Install and Setup R https://www.labkey.org/wiki/home/Documentation/page.view?name=rConfig