Merge pull request #56 from andrewjpage/master

tests pass when config variable output order changes
comment out config files at the top level for mapping and snp calling
Merge pull request #57 from andrewjpage/admin_approval_for_mapping

comment out config files at the top level for mapping and snp calling
Updated help text
Merge pull request #58 from carlacummins/master

Updated help text
Add IVA assembler
Merge pull request #59 from martinghunt/add_iva_assembler

Add IVA assembler
Remove debugging copying of conf file
Use different defaults for IVA assembly options
Merge pull request #60 from martinghunt/add_iva_assembler

Add iva assembler
Updated bacteria_register_and_qc with option to omit ann & ass configs
Added option to omit assembly and annotation configs for bacteria_register_and_qc
Merge pull request #61 from carlacummins/master

Added option to omit assembly and annotation configs for bacteria_register_and_qc
Removed generation of qc config files from form all of the Mapping, RnaSeq, SnpCalling steps
fix command logging
Revert "Removed generation of qc config files from form all of the Mapping, RnaSeq, SnpCalling steps"

This reverts commit db975217c6d5f434eb18054c227dc100a1929daa.
fix tests for qc config and logging time
Merge pull request #62 from andrewjpage/fix_failing_tests

Fix failing tests