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CLM v4.0 installation issues

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I assume as you chose not to install tomcat because you are using WAS and have followed these instructions?
https://jazz.net/help-dev/clm/index.jsp?topic=%2Fcom.ibm.jazz.install.doc%2Ftopics%2Ft_deploy_was.html
Note: If you used IBM Installation Manager to install the CLM applications and during the installation cleared the check box for Install Tomcat 7 with JTS web application, by default, the web application files (.war) are copied into the JazzInstallDir/server/webapps directory. If during installation you selected Install Tomcat 7 with JTS web application, the web application files (.war) are copied into the JazzInstallDir/server/tomcat/webapps directory.
Comments

If I'm using WAS, I will not see that then?
I am on the first step on installation.
http://pic.dhe.ibm.com/infocenter/clmhelp/v4r0/topic/com.ibm.jazz.install.doc/topics/t_s_server_installation_im.html
Is that a defect in documentation? Can I just move on to the database setup? Was I supposed to have WAS installed before all of this? I was going to install before the "Setup WAS" step.

If you install for WAS, you start WAS therefore the menu entries for the server.startup.bat are not there. You can install WAS later. You will point it to the WAR's in the location you shose. You can continue with creating the DB's for now. You need to install WAS as soon as you need to run the applications.