How to install the VienneRNA package 2 on mac OSX 10.8.5

The ViennaRNA package provides a nice set of tools to predict secondary structures of RNA. On mac, the source code needs to be compiled locally. Below follows step-by-step instructions for how to do this. This has been tested on both iMac and MacBook pro.

  1. From the mac app store, get Xcode , which is Apples toolset for building OS X and iOS applications.
  2. In Xcode, choose preferences -> downloads, and download the command line tools.
  3. Log out and back in again to make sure the tools are available in the Terminal.
  4. From http://www.tbi.univie.ac.at/~ronny/RNA/index.html, retrieve the source code for the latest version of ViennaRNA, and unpack.
  5. Open a terminal, and cd to the just unpacked ViennaRNA folder.
  6. Type

 ./configure --without-perl --disable-openmp make sudo make install
This will throw a lot of warnings but still produce a working set of command line tools in the end. When done like this there will be no perl interface support. We have not been able to compile the package with this support not switched off. Also, if you play around with the switches and try adding, e.g. export ARCHFLAGS=”-arch x86_64″, as mentioned in the “Notes for macOS X users” on the ViennaRNA homepage, but get an error message, you may need to remove the folder and re-unpack, before trying again. For those interested in integrating ViennaRNA tools with R, here is a basic R wrapper for RNAplfold, which returns the accessibilities in a matrix object
RNAplfoldR <- function (seq.char, L.in = 40, W.in = 80, u.in = 16) { seq.char <- as.character(seq.char) cmmnd <- paste("RNAplfold -L", L.in, "-W", W.in, "-u", u.in) cat(seq.char, file = paste("|", cmmnd, sep = "")) acc.tx <- read.delim("plfold_lunp", as.is = T, skip = 2, header = F, row.names = 1) acc.tx <- acc.tx[, colSums(is.na(acc.tx)) != nrow(acc.tx)] colnames(acc.tx) <- 1:ncol(acc.tx) file.remove("plfold_lunp") file.remove("plfold_dp.ps") return(acc.tx) }

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One comment on “How to install the VienneRNA package 2 on mac OSX 10.8.5
  1. David Ornelles says:

    Thank you so very much for this nugget of help. It fixed frustration with installation on OS X version 10.6.8.

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