Merge pull request #58 from martinghunt/farm3

added pacbio_assemble_smrtanalysis-2.0.1
Adding mapping for writedb_entry_set
Merge pull request #60 from carlacummins/farm3

Adding mapping for writedb_entry_set
fasta manipulation scripts
Merge pull request #61 from andrewjpage/farm3

fasta manipulation scripts
add chado_dump_genome
extract regions from multifasta
Merge pull request #63 from andrewjpage/farm3

extract regions from multifasta
plasmid identification
Merge pull request #64 from andrewjpage/farm3

plasmid identification
remove snp sites
Merge pull request #65 from andrewjpage/farm3

remove snp sites
identify protein changes at position
Merge pull request #66 from andrewjpage/farm3

identify protein changes at position
identify clusters
Merge pull request #67 from andrewjpage/farm3

identify clusters
Mapping fix test

Edit mapping.yml to try stop nesting of python modules during deployment
Merge pull request #68 from carlacummins/farm3

Mapping fix test
Update to place files in the correct place
Merge pull request #69 from carlacummins/farm3

Update to place files in the correct place