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Author Topic: Problem installing X3DNA in Windows with Cygwin and MinGW/MSYS  (Read 6127 times)

Offline cesarzapata

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Hi Xiang-Jun and other 3DNA users,
It's very nice to meet you, thank your for your time checking this topic. I am a masters student currently working with Molecular Dynamics trajectories of DNA using NAMD and I look forward to use the X3DNA Ensemble in my research.

I am currently trying to install X3DNA in my Windows 7-64 bits-based computer. I have already installed Ruby, and have downloaded both options of Cygwin and MinGW-MSYS. I can't finish the installation. Both programs seem to run and never give me any error message, but when I try the ./find_pairs -h it doesn't do anything.

I don't think have any problems until running the ./x3dna_setup script, setting up the variables and running that source ~/.bashrc which I can't seem to find.

It says:

(3) ./x3dna_setup
to run X3DNA, you first need to do two things:
* set up the X3DNA environment variable
(Are we talking about the variable in Windows? There is also the problem that Linux uses the slash for its directories, while Windows prefers the backslash, in the Windows User Variables should I use the normal slash or the backslash?)
Or perhaps we are talking about the internal variables of the Unix-like shells?
Once the program is installed, will it be able to be called from the normal Windows command line or will it always have to be called through Cygwin or MinGW?

I seem to be lacking a crucial part of the process.





Any help would be greatly appreciated, and thanks a lot again.
« Last Edit: May 08, 2014, 05:37:13 pm by cesarzapata »

Offline xiangjun

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Re: Problem installing X3DNA in Windows with Cygwin and MinGW/MSYS
« Reply #1 on: May 08, 2014, 11:06:20 pm »
Thanks for using 3DNA, and for providing a detailed report of the problems you experienced. The Cygwin version of 3DNA is intended to be run under the Cygwin Terminal window, which provides a Linux-like environment. Specially, it uses slash (/) as the directory separator, and has a user account structure just as in Linux.

One thing I found suspicious is the output from ./x3dna_setup which contains "C:/cygwin64/". I have just re-tested run 3DNA on Cygwin, and the corresponding portion from ./x3dna_setup is as below:

Code: [Select]
  (3) ./x3dna_setup
          to run X3DNA, you first need to do two things:
              o set up the X3DNA environment variable
              o add $X3DNA/bin to your command search path
          for your 'bash' shell, add the following into ~/.bashrc:
          --------------------------------------------------------------
              export X3DNA='/home/xiangjun/x3dna-v2.1'
              export PATH='/home/xiangjun/x3dna-v2.1/bin':$PATH
          --------------------------------------------------------------

Notice the "/home/xiangjun/" part? From my understanding, the output should be something like that instead of "C:/cygwin64".

Run the "Cygwin Terminal" command, and once in the shell, type "pwd". What do you get? What version of Cygwin do you have?

Xiang-Jun
« Last Edit: May 08, 2014, 11:08:36 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: Problem installing X3DNA in Windows with Cygwin and MinGW/MSYS
« Reply #2 on: May 08, 2014, 11:39:42 pm »
Following my previous reply, I realized that you are using Cygwin 64bit while I compiled 3DNA on 32bit. That may be the reason why 3DNA cannot be set up properly. Could you install Cygwin 32bit and try again? I will also have a look on Cygwin 64 later on when I have more time.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cesarzapata

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Re: Problem installing X3DNA in Windows with Cygwin and MinGW/MSYS
« Reply #3 on: May 09, 2014, 07:02:12 pm »
Hello, Xiang-Jun! Thank you so much for your reply. Your comment about the working directory got me thinking and I did a quick search about the initial directory "~" in the Cygwin shell. Turns out I, wrongly, always used cd / to find the tar.gz of x3dna.

I have managed to install X3DNA through Cygwin and I will put my experience here. Perhaps it can help others.

The X3DNA installation through Cygwin has ABSOLUTELY NOTHING to do with the PATH or User variables in windows, everything in the "How to install X3DNA in Linux and Windows" topic has to be done in the Cygwin shell.

First things first, the Cygwin shell is the Cygwin.bat file in C:\cygwin

I did not know that the "~" folder in Cygwin appears in Windows as (Directory where Cygwin is installed)\home\(Your Username)\ , but this appears in Cygwin just as /home/(Your Username)

If you put the download tar.gz in said directory in Windows it will appear in the Cygwin shell immediately and you can continue the steps without any problem. Here are the screens, it's really a very quick process.

Thank you so much for your help Xiang-Jun. I did not try it with Cygwin64 but I think my problem was more of the knowledge of where was the ~ folder.

Here is how the Cygwin shell should look:

Offline xiangjun

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Re: Problem installing X3DNA in Windows with Cygwin and MinGW/MSYS
« Reply #4 on: May 10, 2014, 08:25:13 am »
Quote
I have managed to install X3DNA through Cygwin and I will put my experience here. Perhaps it can help others.

Glad to hear that you have got 3DNA up and running on Cygwin, and thanks for sharing your experience!

If you have further questions in using 3DNA, please do not hesitate to post them on the Forum.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.