The following had build issues:

+# TODO: ABySS, BLAT, BiSearch, Bowtie/1.0.0 (?), FRC_align, FSL, Mothur, NCBI-Toolkit, orthomcl

These just need a version update, and could be synced to latest at some point in future:

+# 2UPDATE: HMMER/3.1, MrBayes/3.2.0, orthomcl, TopHat/?, Trinity/2013-02-25, Velvet/1.2.09