Vahid

I guess it would be also interesting/comprehensive to consider complex STR patterns, where one STR site is composed of multiple repeat expansions. For instance: `(CAG)[*](CAACAG)(CCG)[*]`. The ExpansionHunter paper provides more...

If we take MSDN as a good reference, they have a *path* at the top of the page, and a hierarchy of related pages on the left. Personally I find...

> 1. The first one is the issue that you highlighted - do all providers expose the same cheksum?: They do appear to if the file is not chunked as...

> For the scenario where the user wants to validate that an upload has been performed with no data errors, that could be handled separately, say by providing a verify=True/False...

That solves the integrity verification of the uploaded file. So, we just need to inform a user (in documentation maybe) that upload verification is checksum-based. However, we are still gonna...

Thanks for the updates @jgoecks . Please see if you can make a PR agains [this](https://github.com/VJalili/galaxy/tree/UserBasedObjectStore2) branch; if not, I can update this branch. Besides, I guess we could avoid...

@jgoecks I applied the changes you made on your branch on this branch.

@dannon Thank you! I guess that has fixed it as all tests passed locally.

@dannon I think the patch works fine for integration tests, but it breaks CI unit tests.

The orphan HDA handle is the issue causing the integration test's failure; I guess that is happening when Galaxy is writing metadata to a file.