Merge pull request #184 from teharrison/master

fix out of scope variable
Added external reference ID field to AWE workflow as xref
Merge branch 'master' of github.com:MG-RAST/pipeline
Merge pull request #185 from jaredbischof/master

Added external reference ID field to AWE workflow
Added code to retry a Shock download N times if it fails or the byte size or md5 checksum does not match what is in Shock, where N is a global variable in the script.  Also, added code to check file byte size before md5 checksum because it's quicker and if that fails we don't need to calculate the md5 checksum
Merge branch 'master' of github.com:MG-RAST/pipeline
Merge pull request #186 from jaredbischof/master

Updates and improvemets to torque file download from AWE stage
Re-wrote expanded_sims2overview so that no sorting is required previous to calling this script.  Should save on time and resources.
Merge pull request #187 from jaredbischof/master

Re-wrote expanded_sims2overview so that no sorting is required previous ...
Updated sims2annotation to produce zero-size summary files when input files are zero size.
Added handling for getting e-value exponent where e-value is zero.  Also, added source summary generation code.
Merge pull request #188 from jaredbischof/master

Updates to sims2annotation and updates to expanded_sims2overview that should make this stage parallelizable.
Added new version of sims2annotation under different name for testing in production environment before over-writing the old script version
Merge pull request #189 from jaredbischof/master

Added new version of sims2annotation under different name for testing in...
Fixed formatting issues with source stats summary.  Ready for testing in pipeline.
Merge pull request #190 from jaredbischof/master

Fixed formatting issues with source stats summary.  Ready for testing in...
awe_cluster_parallel.pl: if ucluster generates 0-sized file, copy the input sequence file as the output
Merge pull request #191 from wtangiit/master

awe_cluster_parallel.pl: if ucluster generates 0-sized file, copy the in...
Added checks to make sure prerequisite stages in pipeline actually exist so that deep recursion of the sub_pipeline() does not occur and run berlin out of memory if someone enters a bad pipeline definition.
Merge pull request #192 from jaredbischof/master

Added checks to make sure prerequisite stages in pipeline actually exist...