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Author Topic: How to install 3DNA on MinGW/MSYS  (Read 4845 times)

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/

Offline zainab fadhil

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Re: How to install 3DNA on MinGW/MSYS
« Reply #25 on: October 17, 2016, 09:49:21 pm »
I got the attached response

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #26 on: October 17, 2016, 09:57:55 pm »
So you've sh instead of bash. Try the following:

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

Close, and start a new terminal, try:

Code: [Select]
find_pair -h
This time it should work -- report back how it goes!

Xiang-Jun
« Last Edit: October 17, 2016, 09:59:34 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 #27 on: October 17, 2016, 10:09:33 pm »
I got the same error. Is there a set of instructions that i can use each time i launch the program to avoid this? Or is it better to remove everything and start from the very beginning?
Thx a lot for your help Sir

Offline xiangjun

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Re: How to install 3DNA on MinGW/MSYS
« Reply #28 on: October 17, 2016, 10:35:11 pm »
Then as I mentioned before, just type:

Code: [Select]
source ~/.bashrc
Then all 3DNA v2.3 commands will be available directly. I've tried hard to help you avoid this 'extra' step. For now, it's better that you just remember to run this command.

For new users who has little background on command-line programs, the w3DNA web server may be a better choice.

Thanks for your patience.

Xiang-Jun
« Last Edit: October 17, 2016, 10:40:45 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 #29 on: October 17, 2016, 10:41:13 pm »
So each time, I run it (after typing source ~/.bashrc) as shown in the attached picture, and it is ready to use now, right?
Image is attached.
Thanks a lot Sir for your help.
« Last Edit: October 17, 2016, 11:08:58 pm by zainab fadhil »

 

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.