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Author Topic: How to install 3DNA on MinGW/MSYS  (Read 4837 times)

Offline happytreat14

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How to install 3DNA on MinGW/MSYS
« on: December 12, 2015, 04:56:55 am »
I'm installing x3DNA on a Windows OS. I have downloaded Ruby as well as MingW/MSYS systems.

However, when I typed find_pair -h into the terminal I got the following error:
Code: [Select]
C:\Users\Downloads\x3dna-v2.3-mingw-win.tar\x3dna-v2.3\bin>find_pair -h
Please set the X3DNA environment variable
Run 'x3dna_setup', and visit http://x3dna.org/ for more info.

C:\Users\Downloads\x3dna-v2.3-mingw-win.tar\x3dna-v2.3\bin>x3dna_setup
'x3dna_setup' is not recognized as an internal or external command,
operable program or batch file.

What should I do to resolve this?
« Last Edit: December 12, 2015, 09:25:21 am by xiangjun »

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #1 on: December 12, 2015, 09:54:14 am »
Thanks for using 3DNA.

As shown in the following screenshot, I can reproduce your problem on my Windows 7 system.


You are using Windows native command line shell (cmd) instead of the desired MSYS shell. Did you see the 'M' icon (for MSYS) on your desktop?

Xiang-Jun

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

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #2 on: October 16, 2016, 09:19:26 pm »
Hello Sir,
I am trying to install the program, but i am getting this error. The file x3dna_setup exists in the bin folder. I installed Rubby 2.2.5.
Thanks a lot in advance.

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #3 on: October 16, 2016, 10:42:41 pm »
Click on the Msys2 icon, in the terminal that appears, run the following two commands and report back what you get:

Code: [Select]
pwd
    # in my case: /home/xiangjun
ruby -v
    # in my case: ruby 2.2.4p230 (2015-12-16 revision 53155) [x64-mingw32]

Thanks,

Xiang-Jun


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

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #4 on: October 17, 2016, 10:34:36 am »
I got this.
Thanks a lot.

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #5 on: October 17, 2016, 11:51:45 am »
It appears that Ruby has not been properly installed on your Windows machine, at least the 'ruby' binary is not on your PATH. Could you check to make sure Ruby is directly available as shown in my example?

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

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #6 on: October 17, 2016, 03:32:47 pm »
Do you removing my Ruby instillation and reinstalling it again?

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #7 on: October 17, 2016, 03:40:44 pm »
You could just reinstall and click a button to make sure the Ruby binary available in your PATH at the end of the installation. It should be a straightforward process.

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

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #8 on: October 17, 2016, 06:55:37 pm »
I reinstalled another version and still getting the same message. Will you please tell me what do you mean that the binary file should be in my path? How can i add it?

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #9 on: October 17, 2016, 07:21:38 pm »
I got it to work in my other computer. I got the following image, what is the next step please?

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #10 on: October 17, 2016, 08:03:53 pm »
Good progress! I was trying to show you this link https://github.com/oneclick/rubyinstaller/wiki/Troubleshooting -- it is here just for the record.

Now could you download the 3DNA .tar.gz (tarball) file to your home directory of Msys2, the folder you are in when you simply double-click the Msys2 icon? From your first screenshot, I noticed that you have 3DNA v2.3 installed into your Windows Downloads/ directory. It is more convenient to have 3DNA installed into your home directory.

Follow the instructions at URL http://forum.x3dna.org/howtos/how-to-install-3dna-on-linux-and-windows/, and report back how it goes.

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

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #11 on: October 17, 2016, 08:06:13 pm »
I proceeded further and stuck in the last step as shown in the attachments. Thx for your help.
Or do you suggest redoing the steps that you mentioned in your last reply?

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #12 on: October 17, 2016, 08:08:20 pm »
It seems that I did the steps that you mentioned before and I got the errors that I posted above.
Thx

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #13 on: October 17, 2016, 08:20:38 pm »
Hi,

Thanks for your quick feedback. The issue seems to be related to Windows vs POSIX path names. So, instead of "C:/dssrC/x3dna-v2.3" for the X3DNA environment variable, try the following command (in the terminal after clicking the Msys2 icon):

Code: [Select]
cygpath "C:/dssrC/x3dna-v2.3"
It should report back something like "/home/Ahmed1/dssrC/x3dna-v2.3", i.e., without the C: drive symbol.

Best regards,

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

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #14 on: October 17, 2016, 08:25:01 pm »
I got this. It did not recognize the command.

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.