kraken2

[dpark01]

Adds kraken2 to viral-classify

• adds classify.kraken2 class
• adds metagenomics.kraken2, metagenomics.kraken2_build commands
• adds "kraken2" inputType option to metagenomics.krona
• adds a metagenomics.krona_build option that creates a krona taxonomy db (either with a fresh NCBI pull or with provided taxdump.tar.gz as input)
• separates kraken2 and krakenuniq to two different conda environments, since they cannot coexist in the same conda environment (they write the same binaries to various parts of the path). I've manually verified that both tools still work from the top level either way
• removed some kraken1 (non-uniq) code from metagenomics.py since it wasn't working anyway (though it could possibly be revived by making a third conda environment -- it has the same incompatibility issues that k2 & kuniq have.

[yesimon]

I have a branch with kraken2 and kraken2 depletion somewhere...

[dpark01]

Yeah, I thought it was finally time to at least offer the functionality. I think the only unusual thing about this is how it breaks out into separate conda envs, but it's the only way to deal with multiple kraken tools coexisting in a single docker image. This is one of those areas where our Tool classes are kind of helpful for self-awareness of where a tool is coming from (and making sure to call the correct ancillary scripts: all the kraken tools call several unfortunately same-named bits of software underneath).

If there aren't really objections I may go ahead and push this in soon.