Make it so stages can be run independently

[necrolyte2]

Right now it is quite difficult to get any of the stages to run independently which makes testing each of them hard.

When the pipeline runs(main.py) it runs some functions to properly setup the shell's environment(perl paths, path, vars, ...)

We need to change it such that each stage does not rely on all of that being set, but instead when the virtualenv is activated that is all that is needed for the stages to run(aka, any individual script can run without special paths being passed into it)

[necrolyte2]

Steps to modularize and have simple functional tests

• [x] step1
• [x] host_map
• [x] quality_filter
• [x] ray2_assembly
• [x] iterative_blast_phylo
• [x] orf_filter