using melting under windows

[Nicolas Rodriguez]

-------- Forwarded Message -------- 
Subject:     melting software help 


I'd like to get the MELTING software set up on my Windows computer.  I 
read the README, but I'm a bit of a novice and need more specific 
instructions on getting it set up.  I was able to run the java version 
of the program, but it wasn't able to find the directory with the data 
files.  Thanks for your help. 

Hello,

We recently got some questions about using melting on a windows computer so I am sharing the answer here

in case it can be useful to other users until we make it easier to use melting there.

First, make sure that you downloaded and extracted the latest melting version, right now, it is the 5.1.1 version.

You should note the location where you have extracted melting and open a command prompt (just type cmd in the windows start menu search box).
Once this is done, you need to go to the executable folder, for me:

cd C:\programs\MELTING5.1.1\executable

From there, you should be able to run melting without problem, using the melting.bat script or java:

melting -S ATGTCCTGTGAATATA -E Na=0.1 -P 0.01 -H dnadna

If you are not in the executable folder, the current version of melting will be confused and will complain about not finding the thermodynamic parameter files.
You have several options then. Setup the NN_PATH environment parameter either globally or locally or use the NNPath command line option (the documentation is wrong about this one and talk of the 'nnpath' option).

To set it up globally, see https://www.java.com/en/download/help/path.xml to find the environment variables setup windows. Then, click 'New...' and for variable name, use NN_PATH and for variable value, use the full path to the 'Data' folder that is included in the melting distribution, for me C:\programs\MELTING5.1.1\Data. Now the variable should be set in any new command prompt that you will open, you need to do this only once.

To set it up locally type in the command prompt:

set NN_PATH=C:\programs\MELTING5.1.1\Data

This is only valid for this command prompt and you will have to do it again if you open a new command prompt.

To finish, in fact, if you are not in the executable folder, the current window script will not find the jar file so you would have to use directly java:

java -cp executable\melting5.jar melting.Main -S ATGTCCTGTGAATATA -E Na=0.1 -P 0.01 -H dnadna

or setting the NN_PATH as a command line parameter:

java -cp C:\programs\MELTING5.1.1\executable\melting5.jar melting.Main -S ATGTCCTGTGAATATA -E Na=0.1 -P 0.01 -H dnadna -NNPath C:\programs\MELTING5.1.1\Data


Hope this help, let me know if you have any further questions or problems.

cheers,
Nico