Notes for branch binning_refactor
For now all the analysis tools work (amphora2 and phylophlan were still running when I canceled the test).
The code is pretty messy and might require some cleanup. Some new scripts were added in src/.
We still have to discuss the structure for the output files of the binning, but now all the resulting steps depend on the files being in a single folder (mostly -find the files by their extension and then iterate...)
Dependencies that need to be changed when rebuilding the image:
usearch5 binary is in the IMP git repo now. It needs to inside the container, maybe Yohan can put it on the webdav for now.
Bioperl needs to be version 1.6.924 (includes the fix needed for AMPHORA2), however 1.6.924 is not on apt-get for trusty, in Dockerfile-dependencies the way I installed it with MCPAN can be uncommented.