Moved core scripts back to core scripts folder
Deleted reference to nesi
Fixing bugs in cores scripts and aa_annotate regarding phased vcf file
Stopped deadlock whene the output to the process was greater than the maximum size for the buffer
Mostly working with updates only missing the updates to subprocess to
stop deadlock on the master branch.
Merge branch 'master' of github.com:smilefreak/MerrimanSelectionPipeline
Merge branch 'oo'

Conflicts:
	selection_pipeline/standard_run.py
	selection_pipeline/standard_run_utilities.py
Merged standard_run_utilities
Made changes to standard run to stop deadlock
Fixed problem with stdouts != None
Fixed bug when using stdout as the output from a program
run
Added changes to improve parralelisation for multiple
populations.
Added parallel to selection pipeline
Edits to tutorial document, including queries for James.
Merge branch 'master' of https://github.com/smilefreak/MerrimanSelectionPipeline

Github repo got ahead of my edits.
More edits to tutorial document - up section 4
Fixed problems with multi_population and added new parralelisation
option.
Merge branch 'master' of github.com:smilefreak/MerrimanSelectionPipeline
Started changing the readme added some references to the bibtex,
starting working on miks changes, potential patch for stdoutput error.
Added tutorial data to commit