Merge pull request #217 from jaredbischof/master

 Rather than creating a template without screening, using the -skip option.
Merge pull request #218 from jaredbischof/master

Bug fixes in creating valid AWE workflow document.
Merge pull request #219 from jaredbischof/master

Fixing Shock url for index file download.
Merge pull request #220 from jaredbischof/master

Fixing stage_id to match rna or dna clustering.
Merge pull request #221 from jaredbischof/master

Fixing input/output filenames
Merge pull request #222 from jaredbischof/master

Allowing bowtie screening to be skipped without an error.
Merge pull request #223 from jaredbischof/master

Fixing bugs.
Merge pull request #224 from jaredbischof/master

Moved drisee score insert to job database to the done stage. Added downl...
Merge pull request #225 from jaredbischof/master

Update to stage_id
Merge pull request #226 from jaredbischof/master

Bug fixes
Merge pull request #227 from jaredbischof/master

Fixing stage names and ids
Merge pull request #228 from jaredbischof/master

Adding required package
Merge pull request #229 from jaredbischof/master

Adding another required package.
Merge pull request #230 from jaredbischof/master

Bug fix.
validate metadata: now try both .xlsx and .xls before quitting (user may lie)
Merge pull request #231 from teharrison/master

validate metadata: now try both .xlsx and .xls before quitting (user may lie)
Merge pull request #232 from jaredbischof/master

Edits to only update stage info if stages have progressed.  This prevent...
Merge pull request #233 from jaredbischof/master

Necessary error-checking
Merge pull request #234 from jaredbischof/master

Bug fixes for awe_preprocess_qc.pl
Merge branch 'master' of github.com:MG-RAST/pipeline