Merge pull request #30 from andrewjpage/master

annotation, assembly and farm3 updates
Merge pull request #31 from andrewjpage/master

scripts to perform annotation and assembly
Merge pull request #32 from andrewjpage/master

temp turn off assembly and annotation for all viruses
Merge pull request #33 from andrewjpage/master

virus annotation
Merge pull request #34 from andrewjpage/master

different annotation config file per assembly
Merge pull request #36 from andrewjpage/master

GPL