Merge pull request #250 from keithj/devel

Reading from STDIN for publishing scripts.
Merge pull request #251 from keithj/devel

Bug fix to the iRODs Publisher
Merge pull request #252 from keithj/devel

Get the arguments to ichksum in the correct order.
Merge pull request #253 from keithj/devel

Moving iRODS metadata update inline with publication
Updated MANIFEST
Merge pull request #254 from keithj/devel

Methylation chip support
Merge remote-tracking branch 'wtsi-npg/devel' into devel