fixed bug that left a duplicate column. this is apparently ignored by some ggplot2 versions, but raises an error in the Singularity version

Fixing two relevant issues: chrX occurred twice. And default values from Snake.config.json must be overwritten, otherwise they are used

This fixes issue #1022 of Snakemake (https://bitbucket.org/snakemake/snakemake/issues/1022)

Fixing a Singularity issue with PYTHONPATH (see https://bitbucket.org/snakemake/snakemake/issues/1031)

(works on my computer).

This allows me to more rapidly develp the Dockerfile. Also this commit
includes a separate conda environment which is going to be used within
singularity

Important flag *sn_sites_to_genotype* in the configfile. This overwrites the entry from *Snake.config.json*. The file it points to has to be provided by the user (too big to include into image)

Make reference genome a parameter rather than an input file. This avoids trouble within singularity, where input file existence cannot be checked before the container has been loaded