v1.5.4

Relaxes Trimmomatic defaults (pre-trinity filters) and exposes a few Trimmomatic options, adds a new field to intrahost VCF output, and improvements and updates to Travis CI setup and tool install process.

Details:

• Trimmomatic leading/trailing Q cutoff values have been lowered to a default score of 15. These values, as well as the sliding window size, cutoff, and minlength have been exposed as argparse parameters.
• Add the 'DP' field to the VCF file created at the end of the intrahost component of the pipeline. The field gives, at
  each position, the read depth for each sample.
• Append resource usage to UGER logs
• Remove a lot of non-conda-based fallback tool installers
• Remove Travis caching of conda-installed tools. Also keeps coveralls test coverage consistent.
• Add standalone install_tools.py script that installs tools w/o the need for requirements-tests.txt
• Remove pytest.ini and move into Travis-specific env variables so that developers can specify their own options appropriate to their local dev environment.
• Run flake8 only on pull requests and master branch (skip branch commits)
• Add a requirements-conda.txt file that can be used with conda create to optimize/speed up tool installation