NUPACK is compiled for use in Windows 8

So I just got NUPACK compiled for use natively in Windows 8. The only issue is that you need to manually set the system environment variables to point NUPACKHOME to the folder you extract the NUPACK zip posted bellow to.

Here is the instructions to compile it if yourself courtesy of the people who made NUPACK.

NUPACK Windows Guide

Following has been validated against windows 7/Server 2008 & Windows 8

NUPACK Source Code can be downloaded here. Note, this version is 3.0.4, however for compilation on Windows an older version(3.0.2) will be required.

******NOTE from Jennifer****** Here is the NUPACK 3.0.2 files

Installation of Cygwin

You will need to download and install Cygwin. Choose the appropriate version for your machine(32/64 bit).

You will be prompted to install Cygwin off of the C: directory


During installation of Cygwin, it is important to select the Development options by  double clicking  Default next to Devel, switching it to Install.


Installation of Cygwin can take awhile, as many packages are being installed and configured.

After installation, you may encounter a LibUSB warning, and post install script errors, which you can safely ignore. Click _OK_at the prompt.

Compiling NUPACK

Go to wherever you have downloaded the nupack3.0.2 zip file, right click, and then select Extract All.

Press Browse to select Cygwin home directory, which is where we want the extracted contents of nupack3.0.2 to go.


On Windows, NUPACK must be compiled with special command line arguments.

At this point you will need to double click and open Cygwin terminal, where you will be in the home directory. It is important to note that Cygwin is a Unix emulator, and so the following will commands will be UNIX commands.

We will first need to switch into the nupack3.0.2 directory

Now that we are inside the nupack-3.0.2 folder, we can compile NUPACK using the following command


We now need to set an environment variable NUPACKHOME so that other programs(like Multistrand) will be able to find and run the executables. In order to do this we will edit a hidden file, .profile, adding in a line of text. This ensures that the environment variable will be set every time we open Cygwin.

#ensure that you are using \>\> rather than \>, as \> will overwrite .profile $ echo "export NUPACKHOME=~/nupack3.0.2" \>\> .profile #reload the profile for the current session $ source .profile

At this point the NUPACK executables are runnable on your computer.

Have fun!

zip with the files


Here is a program I just wrote that will set the NUPACKHOME system environment variable for you. You need to run it with elevated privileges. That means for Windows 7 and up run the app as an Administrator. Type in a valid path to the files I posted above or click on “Find NUPACK Folder” ot search for the folder and select the folder you want to use. Enter folder name with out a backslash at the end like this ‘c:\eterna’. Then click on the button “Click to Set Variable” and you should be good to go. Let me know if you have any issues. 

In case anyone is confused since I just realized I did not make myslef clear and now cant edit the original post. At the very end of the original post is a link to the compiled NUPACK files for use natively in Windows 7 and up.

Hello Jennifer, thanks very much for providing the detailed instructions on compiling NUPACK on windows! I would like to download your files to try them out, however, it seems that the links are expired. Could you please resend the link? Also, the figures are not properly displayed. BTW, do you have any idea if the current NUPACK can be installed on windows? Thanks! -Di