gccalcstorage.pl add option to calc tmp and bam output size based on a provided input size rather than actual fastqs
Merge in latest bwa source
UMAKE (SNPCALL) replace OUT_PREFIX with MAKE_BASE_NAME for the base Makefile name.  Add .snpcall, .beagle, .thunder, .vc to the Makefile & conf names so they don't overwrite each other.
Changes from Terry: update gccalcstorage.pl to have a better estimate and update debian/rules.bin to remove 't' from bin directory
GotCloud - add option to run just beagle/thunder; umake - add option to run just each step of snpcall
Add MAKE_OPTS to allow users to add additional options to the make commands used to run the pipelines
Merge branch 'master' of github.com:statgen/gotcloud
Update gccalcstorage.pl to only add a / after a prefix path if a prefix is specified.
Conf.pm - trim trailing spaces from configuration values.
Cleanup snpcall Makefile to remove unused targets.
Fix validation of align test results
Release Version 1.11