sync with develop

minor cleanup in Cufflinks and Tophat easyconfigs (get rid of patches)

add numpy and scipy example easyconfigs

get rid of patch for Tophat, --with-bam option is doing what it should be doing so no patch required

Merge branch 'contrib_Bioinfo_easyconfigs_by_Cedric' of github.com:claczny/easybuild-easyconfigs into contrib_Bioinfo_easyconfigs_by_Cedric

Conflicts:
	setup.py

build SCOOP/PyZMQ with zeromq 2.2.0 (3.2.0 and python interface is

added R easyconfig

clean up easyconfigs, split of XML into separate easyconfig due to dep + develop update

remove exts_filter and exts_defaultclass specs (they belong in EB_R easyblock), cosmetic changes to list of extensions

unstable)

sync order of extensions in easyconfigs, remove XML (has deps), fix default class, add classmap for Bioconductor R packages, fix indentation

add example easyconfigs for NEURON, NWChem, VSC-tools and iomkl

added example easyconfigs + patch files for ALADIN

example easyconfig for Trinity + patch files

Oger

fix MDP file naming + style fixes