adding functional testing

[will-rowe]

Now using the Conda env to manage travis

[will-rowe]

This pull request adds:

• a basic functional test
• travis integration
• test-data
• two minimal conda environments (for testing/running the medaka and nanopolish pipeline variants).

The basic functional test runs through the pipeline as in the documentation. It uses a small example dataset and the output is checked for a consensus fasta file.

Current caveats:

• there is minimal testing of the output - only existence is checked for
• of the two pipeline variants (medaka and nanopolish), the test runner currently onlys tests the medaka variant. The test runner can do either (./test-runner.sh [nanopolish|medaka]) but the decision for just using medaka in Travis was mainly due to the increased runtime needed for nanopolish
• the artic minion error handling needs tweaking to report sys command failures