Update: sepp (pplacer binary)

[sjanssen2]

Work in progress, don't merge!

SEPP depends on pplacer and guppy, which are maintained here https://github.com/matsen/pplacer and written in ocaml. There doesn't seem to be a mechanism in place to compile from source. However, matsen does provide some pre-compiled binaries for Linux and OSX, i.e. version 1.1.alpha-17: https://github.com/matsen/pplacer/releases/tag/v1.1.alpha17 (Sep 23, 2015)

Currently, SEPP bundles older (v1.1.alpha13-0-g1ec7786, 2012-05-21) pre-compiled binaries of pplacer and guppy. On a current Debian system, these binaries through segementation faults, even without any inputs. Therefore, I try to make pplacer available through bioconda (which is lacking an osx package) here: #52395

Once merged, I will change the SEPP recipe in a way that it no longer uses the bundled pplacer and guppy binaries but those available as conda dependency.

Will this change the results? Probably yes, the question is to what degree. Here is a comparison for a 2479 inserted 16S sequence set into the GreenGenes 13.8 reference tree:

1. all sequences are inserted in current and updated version
2. assessing potential differences in the placement positions isn't trivial as a) not all nodes in the reference tree are names, i.e. there is no 1 to 1 mapping possible b) multiple sequences can be inserted into same clades, which will change their topology. I therefore use two metrics:
   1. "tip length": The distance from the direct parent node towards the inserted sequence
   2. "reference distance": first, traversing ancestors towards the root until a node with a numeric name (these are the GG reference tips) is found, then measuring the distance between inserted sequence and this reference node

Of the 2479 sequence

1. 2256 (=91%) get placed at identical positions.
2. maximal "tip length" difference is 0.0645883, maximal "reference distance" is 0.04480039523. For reference, this is about the expected distance of taxa within the same species in the GG tree:
   
3. only 32 (=1%) of sequences get placed at positions that differ more than one tenth of the species radius (~0.05), i.e. 0.005 in the smaller of both above metrics.

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