No doubt he had a gun. Probable that he was holding it but certain it was not pointed at officers. He was shot for failing to heed their warnings to drop it. 

Racial bias probably played a role in the decision to confront him but the course of events beyond that were such that there was no reasonable prospect of obtaining a criminal conviction. But there is a distinction between actions that are criminal versus negligent. A claim for damages would face a lesser threshold in a civil as opposed to criminal trial.

This is not one of the stronger cases of police misconduct involving racial bias in the U.S. but the public protests and property damage that followed are not unexpected. Police departments and the African-American community are both on edge right now and, sadly, things are likely to get worse before they get better. Trump's election is unlikely to have a calming effect.