Fix tests for bedtools, bowtie, bx-python, GenomeAnalysisTK, pysam.
Include more build products in installation.
Fix pysam test.
Include more build products in install.
Upgrade version.  Bug fix: build was installing some products into /opt on
build machine.
Avoid attempting to build cufflinks and qiime--both presently broken.
Upgrade version.
Merge branch 'master' of https://forge.sdsc.edu/stash/scm/aps/biotools-roll

Conflicts:
	src/GenomeAnalysisTK/version.mk
	src/ViennaRNA/version.mk
	src/bedtools/version.mk
	src/biopython/version.mk
	src/bismark/version.mk
	src/bowtie/version.mk
	src/bwa/version.mk
	src/cufflinks/version.mk
	src/fastqc/version.mk
	src/gmap_gsnap/version.mk
	src/htseq/version.mk
	src/linux.mk
	src/picard/version.mk
	src/samtools/version.mk
	src/spades/version.mk
	src/tophat/version.mk
	src/trinity/version.mk