Exit script on failed command. Plus minor changes#12

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mgymrek wants to merge 6 commits intodavek44:masterfrom mgymrek:master

+107-53

Commits on Jan 7, 2016

Replacing space in column header alt_pred
Melissa Gymrek
committed
updating documentation for output of snps_seq1
Melissa Gymrek
committed
adding checks to see that commands completed with 0 exit status
Melissa Gymrek
committed

Commits on Jan 8, 2016

Reverting back to subprocess.call, checking exit status
mgymrek
committed
adding __init__ for relative imports
mgymrek
committed
add no cuda option to install dependencies
mgymrek
committed