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Installing and using RNAfold in Windows

by eupath (Initiate)
on Mar 04, 2013 at 20:08 UTC ( #1021708=perlquestion: print w/ replies, xml ) Need Help??
eupath has asked for the wisdom of the Perl Monks concerning the following question:

I'm a self taught perl-er, using it mainly for bioinformatics research. I need to be able to call functions from the RNAlib in the Vienna RNAfold package, but can't for the life of me get this to work on Windows (RNAfold is written in C/C++, and most documentation is for UNIX/Linux). Anyone know how this is done?

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Re: Installing and using RNAfold in Windows
by aitap (Deacon) on Mar 04, 2013 at 20:49 UTC

    In order to run ./configure; make; make install, you need at least a working POSIX-compatible shell, a compatible version of Make and a working compiler. I'm not sure whether ppm install MinGW provides a POSIX shell (bin/sh or bin/bash); shell is not provided by default in Strawberry Perl.

    Try installing MinGW (is you use ActivePerl), MSYS, adding its bin directory to the PATH environment variable and running sh configure. Maybe it will run properly and create the Makefiles to run make on.

    You can also install Cygwin which can download all the necessary utilities (bash, automake, make, gcc, perl) by itself (and for itself) and build the required program just like under Linux.

    Sorry if my advice was wrong.
Re: Installing and using RNAfold in Windows
by Anonymous Monk on Mar 04, 2013 at 22:55 UTC
    you should get msys, you can get it from or here

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