Question

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?

Answer 1

The Vienna RNA tools, including RNAfold, can be installed locally by compiling the source code available on the GitHub page. It may require troubleshooting and addressing dependencies, but successful installations and batch processing have been reported by many users.

Step-by-step explanation:

The Vienna RNA tools, including RNAfold, can be installed locally by compiling the source code available on the GitHub page. It is true that large C/C++ projects with third-party dependencies can be challenging to compile, but following the installation instructions provided with the source code can help navigate through any difficulties. Some necessary header files may not be present on a Windows system, but these can usually be obtained through package managers or by manually downloading and installing them.

Alternatively, you can try using Anaconda and bioconda to install viennarna. If the software is not found, it may be necessary to check if all the required channels are enabled in bioconda and that the correct version of Anaconda is being used. It is also worth consulting the online documentation and user forums to see if other users have encountered similar installation issues and found solutions.

While it may require some troubleshooting, many users have successfully installed the Vienna RNA tools locally and used them for batch processing.