removed puppet-r as submodule
working r submodule
tidy up submodule definitions
updated shell provisioner for VCF
provisioning of vcf and bed tools
fixed shell provisioning for bedtools
reverted cython item
working for vcf  abd bed tools now
Updated README.md
Merge branch 'master' of https://github.com/cfljam/statgen_py_vm
Updated README.md
modified ipython privilege status to run as default user
added Gist Notebook
modified provisioning conditionals and vcftools config for perl tools
set vcftools PERL5LIB
added vcflib
Updated README.md
Updated README.md
changed to git clone as https
Updated README.md