Update conda environment and include packages r-pheatmap, bioconductor-complexheatmap, and r-gplots needed by plot-clustering.R

Upgrade environment to get WhatsHap 0.17, which correctly handles haplotagging when chromosomes are missing in VCF file

Update conda environment: this fixes an error "assert_that: assertion must return a logical value", presumably due to a new version of r-assertthat. Also, add scipy (needed for ploidy estimation script) and whatshap (needed for haplotagging).

Update GenomicAlignments package to 0.14, the previous environment caused the following problem in StrandPhaseR:

Warning message:
multiple methods tables found for ‘rglist’
Working on chromosome chr2
 Loading data for 58 WCregionsError in validObject(.Object) :
  invalid class “GAlignments” object: undefined class for slot "NAMES" ("characterORNULL")
Calls: strandPhaseR ... phaseChromosome -> loadMatrices -> bamregion2GRanges
Execution halted