Added the feature of reading file or plate names from STDIN. This
makes publish_infinium_file_list.pl redundant.
Use git describe --dirty --always

Use same version checking regexp for both Perl and Ruby.
Fixed inverted test for undef.
Include STDERR of wrapped program in the logged error message.
Merge pull request #250 from keithj/devel

Reading from STDIN for publishing scripts.
Bug fix to the iRODs Publisher to ensure that ichcksum calls force
checksum recalculation and that files are overwritten when requested.
Merge pull request #251 from keithj/devel

Bug fix to the iRODs Publisher
Get the arguments to ichksum in the correct order.

This was not raising an error in the tests. How?
Merge pull request #252 from keithj/devel

Get the arguments to ichksum in the correct order.
Added new method iRODS::copy_object
Moved iRODS metadata addition inline with file publication.

Added more tests for behaviour when overwriting files.
Added new test files omitted from previous commit.
Merge pull request #253 from keithj/devel

Moving iRODS metadata update inline with publication
Added tests on updating manual QC metadata for Sequenom results.
Added some comments on metadata cache behaviour.
Updated MANIFEST
Added support for Infinium methylation chips.
Added support for the new inline metadata updates to the publishing
scripts. I missed these in the last commits.

Added a new --reference-zone command line argument to
publish_fluidigm_genotypes.pl
Merge pull request #254 from keithj/devel

Methylation chip support
Replace the default value for the reference_zone attribute.