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I'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, it mentions that there are pre-compiled versions of the software available for all major operating systems, however the site seems to be down. All that's still accessible is the GitHub page with source code access.

From my experience, trying to get large C/C++ projects, that often have quite a few third party dependencies, to compile is a huge pain. And even the Python "version" (really a Python wrapper around the C++ code) doesn't install with pip, despite having a compiler available (and found by pip), there are quite some header files that aren't on my Windows system that it complains about--and I've generally never had a problem with pip not being able to install other Python packages, even ones that are internally mostly C/C++. Even installing Anaconda, then bioconda, and then trying to install "viennarna", it isn't found. I'm beginning to think that these tools are just broken other than on the sorts of workstations on which they were developed, which already have all the necessary dependencies and headers.

Has anyone else managed to get a local install of these tools working?

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    $\begingroup$ It think this question is ways better fitted for the bioinformatics community: bioinformatics.stackexchange.com Shall I migrate it? $\endgroup$
    – Chris ♦
    Sep 15 at 6:08
  • $\begingroup$ I can access the website normally, and I have been using precompiled ViennaRNA on Windows without any problems. $\endgroup$
    – Domen
    Sep 15 at 8:09
  • $\begingroup$ @Chris I didn't know there was a separate bioinformatics community, yes it would be better migrated there. $\endgroup$
    – biohacker
    Sep 15 at 19:09

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Against my better nature (I think that this is a question about software, not biology), I offer:

https://www.tbi.univie.ac.at/RNA/#download

Download screenshot

This download works for me to get the precompiled packages.

You could also try here (for a few days): davidleader.net/Wienershnitzel/index.html

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    $\begingroup$ I have edited the answer to remove the irrelevant pieces Domen is responding to. $\endgroup$
    – Maximilian Press
    Sep 15 at 12:09
  • $\begingroup$ And so we are left with the situation that a helpful and correct answer to a question, despite being off-topic, is sitting on -1. And all because I pointed out that most modern bioinformatics is written on and for Unix-type operating systems, which does not include MS Windows but does include another which also has widespread support for consumer software. $\endgroup$
    – David
    Sep 15 at 18:54
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    $\begingroup$ @biohacker — I'll download again and mount it on a webpage for download. $\endgroup$
    – David
    Sep 15 at 21:27
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    $\begingroup$ @biohacker Try davidleader.net/Wienershnitzel/index.html $\endgroup$
    – David
    Sep 15 at 21:38
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    $\begingroup$ Another few options: run Vienna on a virtual machine with a (totally free) installation of linux - basic ones like Ubuntu or Mint are very easy to install. Run on a Linux distro designed to run from USB drives - Puppy linux used to be the goto there, dual boot a linux distro, or (best IMO) run one of the several docker containers for viennaRNA . $\endgroup$
    – bob1
    Sep 15 at 22:27

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