Merge pull request #49 from wtsi-npg/devel

Devel
Merge pull request #53 from wtsi-npg/devel

pull from Devel for release 10.4
Merge pull request #55 from wtsi-npg/devel

Devel
Merge pull request #57 from wtsi-npg/devel

Devel
Merge pull request #59 from dkj/devel

Refactoring and code removal
Merge pull request #60 from wtsi-npg/devel

Devel
Merge pull request #61 from wtsi-npg/master

v10.7
use Perl from PATH