Try this: check the file content before Upload to Galaxy. Try converting bam to sam format with Samtools. You could also try sorting the bam. If it fails for you locally, then it would fail in Galaxy.
Or, try this: directly Upload the cram data to Galaxy. Most tools do not directly use cram format, but you can convert cram to bam in Galaxy with the tool Samtools view.
For either, try letting the Upload tool auto detect the format first. If that doesn’t work, you can assign the datatype instead (during Upload – not sure if you tried that already for the bam or not).
I’m also not exactly sure how good we are at auto detecting cram format right now… but I’ll test that later today or tomorrow since am now curious. If any usage deviates from the above – I’ll post back.
It would be best to do this at the UseGalaxy.org or UseGalaxy.org.au server right now. The UseGalaxy.eu server is undergoing some admin changes this week, and some odd behavior is expected until the banner clears. It is easier to troubleshoot without complicating factors.
Thanks!