I'm in the process of installing miRDeep2_0_0_8 on Ubuntu 14.04.

I've installed the Vienna package (RNAfold 2.1.9), and RNAfold starts when I type "RNAfold" making me think that the installation has been successful. However, the miRDeep2 install hangs on the Vienna package.

When I run "perl install.pl" within the miRDeep2 directory it passes gcc and bowtie checks, then I get this:

RNAfold 2.1.9

Calculate minimum free energy secondary structures and partition function of
RNAs

Usage: RNAfold [OPTIONS]...

[ Followed by the RNAfold options/help file ]

Then:

Downloading Vienna package now

Vienna package not found at  http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-1.8.4.tar.gz
Please try to download the Vienna package from here http://www.tbi.univie.ac.at/RNA/RNAfold.html

Vienna is installed, so it shouldn't need to download RNAfold - is this a Vienna version problem? miRDeep attempts to download Vienna 1.8.4, but I have 2.1.9 installed.

Any insight into the problem is appreciated, I'm running out of ways to google this problem!