Split checksum file into chunks

[TamaraNaboulsi]

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Requirements

• Filling out the template is required.
• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
  • if you change the schema you must patch the test databases as well, see Updating the schema
  • the PR must not fail unit testing

Description

Splitting the large checksum file into smaller ones.

Use case

Timeout errors are popping up in the Checksum step of the pipeline because of the 'LOAD DATA INFILE' command being run on a very large file. This fix consists of splitting the big file into multiple smaller ones and running the command on each. At the end, the code combines these smaller files into 1 to revert back to the previous state of things at the end of running.
This change is also accompanied by another in the DB model (ensemb-py) to set the engine for the checksum_xref table to MyISAM as this decreases the probability of getting the error.

Benefits

Probability of errors decreases.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes.

Testing

• Have you added/modified unit tests to test the changes?
• If so, do the tests pass?
• Have you run the entire test suite and no regression was detected?
• TravisCI passed on your branch

Dependencies

If applicable, define what code dependencies were added and/or updated.