Affy gene normalisation bug fixed.
Fix cna-segment.R tool id
Generate-phenodata and norm-prenormalized modified so that special
characters are trimmed off.
Remove testng from build.xml
Remove intact and reactome tools.
Script for migrating old contents2.txt annotations to new directory and
yaml format.
Changed default parameter value for CNA-seq segmentation tool.
Merge remote-tracking branch 'upstream/master'