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!