-uses samtools v1.3, jellyfish 2.2.6, and trimmomatic 0.36
-seqtk now used for fastq->fasta conversions
-updated compute resource monitoring routines that leverage collectl
-included utilities to examine strand-specificity of the rna-seq reads:
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Examine-Strand-Specificity-Trinity carefully checks formatting of 'samples_file' to ensure it uses all the samples (dealing w/ non-unix text-editor formatting issues that can bundle the entire text file into what looks like a single line of text)
-Docker image updated to include salmon for abundance estimation
-refined use of bowtie2 in chrysalis clustering and various updates to improve long-read support.
