Bioconda recipes for missing tools

[apeltzer]

We should have bioconda recipes for every tool used in the pipeline, (some of them are already there). This allows us to create a single Dockerfile/Singularity container with just a couple of lines of code and directly link this to the version of the pipeline with a simple GitHub /Git tag in the future.

List of recipes already there (some pull requests of mine are pending for some of the tools required here):

https://github.com/bioconda/bioconda-recipes

ToDo List:

• Schmutzi
• snpAD
• PMDTools
• SequenceTools
• AdapterRemovalFixPrefix
• CircularMapper

[apeltzer]

Schmutzi is a terribly tricky task unfortunately, cross linking the efforts we did with @grenaud on this:

bioconda/bioconda-recipes#10026

Unfortunately the bamtools library seems to be quite dead by now and nobody fixes issues there anymore.