--> In m.txt is a set of parameters that has been provided.

--> I verified based on the following jazz.net forum discussion, where one of the users did face a similar issue.

https://jazz.net/forum/questions/172748/repotools-set-up-of-jts-always-crashes-with-a-nullpointerexception

Here is the steps that was taken by one of the users there to resolve:

*****

It turns out that the change to /etc/security/limits.conf hadn't been saved in the snapshot I ran the above test from.
Looking at the server logs, I saw the 'too many open files' messages. Once I updated limits.conf and restarted the machine,
I was able to run through the command line setup successfully.

*****

However, I verified this and here is the settings that I had:

*****

* hard nofile 755360
* soft nofile 755360
* hard nproc 200000
* soft nproc 200000

*****

These are the limits.conf file additions made when the server was configured.

-->

The install is failing due to possible missing properties:

*****

CRJAZ2247E There was an error executing setup for the application "Rational Jazz Team Server (https://test.com:9443/jts)": "null". Check the log for more details.
java.lang.NullPointerException
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.getReference(ScriptableSetupWizardProcessor.java:1466)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.createRequestArgs(ScriptableSetupWizardProcessor.java:1407)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.execute(ScriptableSetupWizardProcessor.java:1195)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.doCall(ScriptableSetupWizardProcessor.java:1188)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.invokeSetupService(ScriptableSetupWizardProcessor.java:894)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStepChoiceOptions(ScriptableSetupWizardProcessor.java:770)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStepChoiceOptions(ScriptableSetupWizardProcessor.java:761)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStepChoiceOptions(ScriptableSetupWizardProcessor.java:761)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.processChoices(ScriptableSetupWizardProcessor.java:607)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStep(ScriptableSetupWizardProcessor.java:582)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.process(ScriptableSetupWizardProcessor.java:355)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.runSetup(ScriptableSetupWizardProcessor.java:213)
    at com.ibm.team.repotools.commands.remote.internal.SetupCommand.execute(SetupCommand.java:93)
    at com.ibm.team.repotools.command.AbstractCommand.execute(AbstractCommand.java:68)
    at com.ibm.team.repotools.rcp.internal.RepositoryToolsApplication.run(RepositoryToolsApplication.java:816)
    at com.ibm.team.repotools.rcp.internal.RepositoryToolsApplication.start(RepositoryToolsApplication.java:891)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:369)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
    at java.lang.reflect.Method.invoke(Method.java:611)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:620)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:575)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1408)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1384)

CRJAZ2236E There was an error executing setup: "Internal error"
Check the log at "/opt/IBM/JazzTeamServer/server/repotools-jts_setup.log" for more information.
com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$ScriptableSetupException: Internal error
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.runSetup(ScriptableSetupWizardProcessor.java:218)
    at com.ibm.team.repotools.commands.remote.internal.SetupCommand.execute(SetupCommand.java:93)
    at com.ibm.team.repotools.command.AbstractCommand.execute(AbstractCommand.java:68)
    at com.ibm.team.repotools.rcp.internal.RepositoryToolsApplication.run(RepositoryToolsApplication.java:816)
    at com.ibm.team.repotools.rcp.internal.RepositoryToolsApplication.start(RepositoryToolsApplication.java:891)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:369)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
    at java.lang.reflect.Method.invoke(Method.java:611)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:620)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:575)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1408)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1384)
Caused by: java.lang.NullPointerException
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.getReference(ScriptableSetupWizardProcessor.java:1466)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.createRequestArgs(ScriptableSetupWizardProcessor.java:1407)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.execute(ScriptableSetupWizardProcessor.java:1195)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor$AbstractServiceHandler.doCall(ScriptableSetupWizardProcessor.java:1188)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.invokeSetupService(ScriptableSetupWizardProcessor.java:894)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStepChoiceOptions(ScriptableSetupWizardProcessor.java:770)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStepChoiceOptions(ScriptableSetupWizardProcessor.java:761)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStepChoiceOptions(ScriptableSetupWizardProcessor.java:761)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.processChoices(ScriptableSetupWizardProcessor.java:607)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.executeSetupStep(ScriptableSetupWizardProcessor.java:582)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.process(ScriptableSetupWizardProcessor.java:355)
    at com.ibm.team.repository.service.internal.setup.processor.ScriptableSetupWizardProcessor.runSetup(ScriptableSetupWizardProcessor.java:213)


*****

-->

I was trying to use LDAP and was not disabling ADMIN user and trying to activate the "contributor" trial licenses.

I succeeded in running through a complete command line setup by disabling the ADMIN user and using the full licenses instead of contributor. With this combination the NPE is not hit.