Changed _initialize_env.SCRATCH_DIR to _initialize_env.VIGOR_SCRATCH_DIR to avoid changing /usr/local/scratch (which other programs use). Removed all unused, vigor-cleanup functions.
Changed _initialize_env.SCRATCH_DIR to _initialize_env.VIGOR_SCRATCH_DIR to avoid changing /usr/local/scratch (which other programs use). Removed all unused, vigor-cleanup functions.

pjotrp/cloudbiolinux,chapmanb/cloudbiolinux,elkingtonmcb/cloudbiolinux,elkingtonmcb/cloudbiolinux,AICIDNN/cloudbiolinux,pjotrp/cloudbiolinux,averagehat/cloudbiolinux,joemphilips/cloudbiolinux,heuermh/cloudbiolinux,kdaily/cloudbiolinux,heuermh/cloudbiolinux,elkingtonmcb/cloudbiolinux,heuermh/cloudbiolinux,chapmanb/cloudbiolinux,pjotrp/cloudbiolinux,kdaily/cloudbiolinux,rchekaluk/cloudbiolinux,averagehat/cloudbiolinux,joemphilips/cloudbiolinux,kdaily/cloudbiolinux,chapmanb/cloudbiolinux,kdaily/cloudbiolinux,elkingtonmcb/cloudbiolinux,AICIDNN/cloudbiolinux,lpantano/cloudbiolinux,heuermh/cloudbiolinux,lpantano/cloudbiolinux,pjotrp/cloudbiolinux,chapmanb/cloudbiolinux,AICIDNN/cloudbiolinux,averagehat/cloudbiolinux,rchekaluk/cloudbiolinux,joemphilips/cloudbiolinux,joemphilips/cloudbiolinux,rchekaluk/cloudbiolinux,averagehat/cloudbiolinux,AICIDNN/cloudbiolinux,rchekaluk/cloudbiolinux,lpantano/cloudbiolinux