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Author Topic: How to install 3DNA on MinGW/MSYS  (Read 14434 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.

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #15 on: October 17, 2016, 08:47:10 pm »
Weird. The cygpath command is available in my case.

Based on the output of x3dna_setup you provided, C:/dssrC/x3dna-v2.3, the x3dna-v2.3 directory is not under your Msys2 home directory. Your could run "C:/dssrC/x3dna-v2.3/find_pair -h" to get some feedback.

Anyway, what's the output of the following command?

Code: [Select]
ls /c/dssrC/x3dna-v2.3
Alternatively, do you know how to change to the C:/dssrC/x3dna-v2.3 directory in Msys2, and then type:

Code: [Select]
pwd
What's the output?

Xiang-Jun
« Last Edit: October 17, 2016, 08:55:13 pm by xiangjun »
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 #16 on: October 17, 2016, 08:53:38 pm »
It is attached here

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #17 on: October 17, 2016, 08:55:45 pm »
The answer to this question "Alternatively, do you know how to change to the C:/dssrC/x3dna-v2.3 directory in Msys2, and then type:" is no (unfortunately). I can try though.

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #18 on: October 17, 2016, 08:58:20 pm »
OK, type the following three commands:

Code: [Select]
export X3DNA=/c/dssrC/x3dna-v2.3
export PATH=$X3DNA/bin:$PATH
find_pair -h

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 #19 on: October 17, 2016, 09:04:10 pm »
Screen shot attached.

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #20 on: October 17, 2016, 09:11:01 pm »
Success!

To make the settings permanent, please copy-and-paste the two export commands to your ~/.bashrc file. For your convenience, please do the the following:

Code: [Select]
echo 'export X3DNA=/c/dssrC/x3dna-v2.3' >> ~/.bashrc
echo 'export PATH=$X3DNA/bin:$PATH' >> ~/.bashrc

To see the results, type this command:

Code: [Select]
tail ~/.bashrc
Please 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 #21 on: October 17, 2016, 09:20:11 pm »
Really!!!
The response is attached.

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #22 on: October 17, 2016, 09:32:36 pm »
Great! Now close the current terminal, and click the Msys2 icon to start a new one. In the newly opened terminal shell, you should be able to run 3DNA commands directly as below:

Code: [Select]
find_pair -h
That's it!

It helps if you could summarize the steps we have gone through, from a new user's perspective, to improve your understanding of the process and to benefit other potential 3DNA users. In principle, this installation process should not take more than a few minutes for users with some command-line skills. In reality, as you now underwent, it could take much longer, and the process could be quite stressful. It is with such user-support experiences that I've decided to make each of the 3DNA v3 programs (DSSR/SNAP) self-contained.

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 #23 on: October 17, 2016, 09:39:56 pm »
I closed it and then  run the file and got this. There is an error that i can't see.

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #24 on: October 17, 2016, 09:45:25 pm »
Well, it always takes longer than expected. Your installation of Msys2 seems a bit weird to me.

Try the following:

Code: [Select]
echo $SHELL
Whatever the case, you could simply:

Code: [Select]
source ~/.bashrc
And then the 3DNA v2.3 commands would be available:

Code: [Select]
find_pair -h
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.