Interface seems to have changed. There may still be missing changes.

Made genome configurable for GRO-seq, tried to debug rpy2 uncachable
exceptions.

Also updated gene list names.

Also updated one gene list name.

This is to limit clutter from old analyses.

Also did a little code cleaning and added a gene list to the small RNA
pipeline.

The desired normalizer for bigwig files was not actually used.

Factorized linking to raw data.

It turns out that using `include:` can fail when there are symlinks in
the path to the snakefile.

This makes the DE results easier to compare with those from small
RNA-seq.

For RNA-seq and GRO-seq, log and data directories are now subdirectories
of output directories. local_annot_dir also moves as subdirectory of
GRO-seq output.

Started to apply to RNA-seq and GRO-seq technique used in small RNA-seq.

I should check to be sure that this is the correct thing to do. The
other possibility would be to sum using agg:
https://stackoverflow.com/a/35403903/1878788

lfcMLE may bring problems with low-expressed genes.

Also:
- Boxplots with labels turned 90 degrees
- do_deseq2 returns size factors