Amptk

* add `--pseudopool` option to `amptk dada2`

* bug fix for `amptk summarize` if taxonomy not present 57
* add FASTA extraction step to install 59
* add chimera detection options to dada2 60
* fix DADA2 for ion torrent data, in newer versions of dada2 the quality score issue has been fixed, so can now use quality scores during sample inference.

* fix for `amptk summarize` --> rewrote script
* large update to taxonomy assignment, switched to vsearch for all global alignment steps
* update to all taxonomy databases, the downloads are larger but the data should be more robust
* update to the COI bold2utax method in docs
* update to `amptk database` and the command line options
* bug fixes along the way

This is a major reorganization of the code so it is "properly packaged" and can be installed with pip and hopefully conda. After v1.2.4 there were apparently changes to conda that would not allow the scripts to build with the previous code organization. I've then also fixed a few of the bugs that have shown up more recently, including:
* The py2 error in the `bold2amptk.py` accessory script https://github.com/nextgenusfs/amptk/issues/40
* the `edlib` version bug reported several times after edlib updated how it stores the version info https://github.com/nextgenusfs/amptk/issues/46

* bug fix where `edlib` version was not properly parsed due to changes upstream, fix is backwards compatible and hopefully future version compatible as well. This was error in 40 and several other "offline" emails.
* update to `amptk stats` to generate interactive `html` output for NMDS output, allowing users to identify which samples correspond to which point on the graph. This requires `r-plotly, r-htmltools, and r-dt` -- however should be all installed through bioconda
* bug fixes for `amtpk SRA-submit`
* improve error/logging in `amptk taxonomy`
* fix R scripts to be compatible with R>3.4.1 -- somehow different way of parsing the command line arguments. Also removed the "auto-install" function in the R scripts -- this was meant to be a convenience but didn't always work.

* trying to fix tab error that bioconda didn't like, version bump accordingly.