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Author Topic: Re: How to install 3DNA on Windows?  (Read 4696 times)

Offline MingyuSun

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Re: How to install 3DNA on Windows?
« on: March 11, 2016, 09:05:31 am »
I am sorry for keep bothering you for silly question. After I run"./x3dna_setup", I can't do the key parts colored red. I put my case in the attachments. I can't find ~/.profile. is it just be in linux? It seems that I can't find that under windows.

Offline xiangjun

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Re: How to install 3DNA on Windows?
« Reply #1 on: March 11, 2016, 10:06:57 am »
Please follow a thread though instead of jumping around. Let's stay in the current thread until you've really got 3DNA up and running.

Please perform the following steps:

  • Double-click the msys icon to get the shell
  • Within the opened terminal, type the following commands strictly:
    Quote
    echo    'export X3DNA=$HOME/x3dna-v2.3' > .profile
    echo     'export PATH=$X3DNA/bin:$PATH' >> .profile
    cat     .profile
  • Close the shell
  • Double-click the msys icon to open another shell
  • In the opened terminal, type: fiber -h
« Last Edit: March 11, 2016, 09:31:26 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline MingyuSun

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Re: How to install 3DNA on Windows?
« Reply #2 on: March 11, 2016, 09:14:47 pm »
Sorry for that and sorry for failing to notice your reply in time, which may due to that I forgot to choose the e-mail notification. There may be something wrong for me. If I double-click the msys icon to get the shell and type the commands, I will see fig. install 04. And then I close the shell,
double-click the msys icon to open another shell, type "fiber -h", I will see install 06. I also tried to do the first three steps of installation, and type the commands you gave me in the reply, that is fig. install 05, but I meet the same case as fig. install 06.

Offline xiangjun

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Re: How to install 3DNA on Windows?
« Reply #3 on: March 11, 2016, 09:30:50 pm »
Did you notice the *space* in the original commands I gave?
 echo   export, and cat     .profile

Now I've modified my previous reply with more spaces to make it clear.

You could use tab or many than one space.

Try again.
« Last Edit: March 11, 2016, 11:46:15 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline MingyuSun

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Re: How to install 3DNA on Windows?
« Reply #4 on: March 11, 2016, 10:13:56 pm »
I am really grateful for you! I am very excited now! Thank you very much for your great creation and patience! I am exploring happily now!

Offline xiangjun

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Re: How to install 3DNA on Windows?
« Reply #5 on: March 11, 2016, 10:18:56 pm »
Congratulations! Now you have 3DNA installed. You could move/copy x3dna-dssr.exe into the x3dna-v2.3/bin directory so it can also be directly accessible.

For your own benefit (and other new 3DNA users), please summarize the long process you have gone through.
« Last Edit: March 11, 2016, 11:47:31 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline MingyuSun

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Re: How to install 3DNA on Windows?
« Reply #6 on: March 12, 2016, 12:41:17 am »
I am sorry for failing to notice your reply in time again. As for the summary, I will definately do with pleasure! 3DNA is a great work! Could I leave that for my birthday on Mar. 20th, since I have been doing something myself in celebration for the day ever since I was 17? And this year, I want to do the summary for my birthday. Before that, I will enjoy my journey, trying to get more about it and providing more information at that time.
But I can also do it right away if you hope so.

Yours
Mingyu
« Last Edit: March 12, 2016, 12:44:58 am by MingyuSun »

Offline MingyuSun

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Re: How to install 3DNA on Windows?
« Reply #7 on: March 15, 2016, 07:55:03 am »
I tried install 3DNA with Cygwin for several times to finish my homework I left here, only to fail again. I found this topic and I followed, http://forum.x3dna.org/howtos/problem-installing-x3dna-in-windows-with-gygwin/ , in fact, I also tried several changes after the failure, but still succeed. I tried this way too. I put the sreenshots here. What's wrong again?
Quote
Double-click the msys icon to get the shell
Within the opened terminal, type the following commands strictly:
Quote
echo    'export X3DNA=$HOME/x3dna-v2.3' > .profile
echo     'export PATH=$X3DNA/bin:$PATH' >> .profile
cat     .profile
Close the shell
Double-click the msys icon to open another shell
« Last Edit: March 15, 2016, 08:41:33 am by MingyuSun »

Offline Maya12

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Re: How to install 3DNA on Windows?
« Reply #8 on: July 01, 2016, 08:26:39 am »
I  tried to install X3DNA on my PC with windows.  and tried to install it using the commands as given in the picture. It says cat: command not found. Please help me in this regard. Also the msys icon is there in the file, not installed in the desktop . When I am double clicking on this icon in the file, an image file is opening instead of the shell. The shell I opened by directly clicking on sh (application file).

Offline xiangjun

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Re: How to install 3DNA on Windows?
« Reply #9 on: July 01, 2016, 11:48:56 am »
Hi,

Thanks for using 3DNA. I feel your frustration in getting 3DNA up and running. Let's see how we can work together to get over the hurdle.

I am a bit surprised that the 'cat' command is not found in your MinGW/MSYS installation. However, it is not essential for running 3DNA. Please try the following commands:

Code: [Select]
source .profile
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 Maya12

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Re: How to install 3DNA on Windows?
« Reply #10 on: July 01, 2016, 12:29:56 pm »
Thank you for your reply.
I tried all those commands but nothing happened, though fiber as well as fair_pair exist among files in X3DNA directory. All the three Ruby, MinGW and X3DNA are in C:/.
Can you suggest some way to install X3DNA properly.


Offline xiangjun

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Re: How to install 3DNA on Windows?
« Reply #11 on: July 01, 2016, 01:32:25 pm »
Thanks for your quick follow-up.

Where is 3DNA installed? What's the output of running the "x3dna_setup" Ruby script? There seems no shortcuts. Let's start from the very beginning for trace where the problem is.

Alternatively, you may want to install Cygwin which is closer to a Linux environment. A local expert with command-line skills would certainly be helpful.

Since this thread is becoming quite long, please start a new one. Based on this experience, I will consider to write a new "Howto" post with details on setting up 3DNA on Windows.

Best regards,

Xiang-Jun

« Last Edit: July 01, 2016, 03:04:46 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline MingyuSun

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Re: How to install 3DNA on Windows?
« Reply #12 on: July 02, 2016, 04:58:31 am »
Dear Mayar12,
I am not sure if you have problem in this step,

echo    'export X3DNA=$HOME/x3dna-v2.3' > .profile
echo     'export PATH=$X3DNA/bin:$PATH' >> .profile
cat     .profile

or you may not install MINGW.

I recorded my experience in For Novice, it might give to some hints.
http://forum.x3dna.org/howtos/for-novices/msg2110/#msg2110
You can just read the following part:
Installation with MinGW
1, install msys
•   Following the link Getting Started, download the GUI installer 'mingw-get-inst'. Use defaults options, except at the "Select Components" section, be sure to pick "MSYS Basic System" so that both MinGW and MSYS are both installed at the same time.
•   Then install the latest version with Ruby (v1.9.3) with "Ruby Installer". In the "Installation Destination and Optional Tasks" section, be sure to select "Add Ruby executables to your path", and "Associate .rb and .rbw files with this Ruby installation".(ref04)
Notice:
1, there is a detailed instruction here, the only difference is that I did not see “blur”, but I presumed that it was not a serious problem since I installed successfully at last.
http://www.mingw.org/
2, if you can only see MinGW installer icon (fig.MinGW01), you have not installed it, you should see MinGW shell icon (fig.MinGW02) after successful installation.
3, double click MinGW installer icon (fig.MinGW01), make sure you pick "MSYS Basic System", then, chose “Apply Changes” in the Installation in the upper left, you can get MinGW shell icon (fig.MinGW02)

2, install Ruby
http://rubyinstaller.org/downloads/
You can find it there, and since there is one installer for the case that you are not sure yourself, novices should be able to cope with that. Just follow the quoted instruction.

3, install 3DNA
1, double click msys icon to open a new shell, type ‘pwd’, which show your home directory (mine is /home/Administrator)
 '/home/administrator' is your home directory. On Windows, it should be in C:\MinGW\msys\1.0\home or something like that. (ref05) not C:\Users\Administrator.
2, move (or copy) the downloaded file (tarball x3dan-v2.3-mingw-win.tar.gz) into your home directory (depression is not needed), that is C;\MinGW\msys\1.0\home. If you did it correctly, you would see something after typing “ls –l”(lower case L) in the shell.
3, run “tar zxvfp x3dna-v2.3-mingw-win.tar.gz”
4, run “cd x3dna_v2.3/bin (or other ~_v~)
5, run “./3dna_setup”
6, as for the instruction get see (fig.install01,the upper part),
1.   Double-click the msys icon to get the shell
2.   Within the opened terminal, type the following commands strictly:
Quote
echo    'export X3DNA=$HOME/x3dna-v2.3' > .profile
echo     'export PATH=$X3DNA/bin:$PATH' >> .profile
cat     .profile
3.   Close the shell
4.   Double-click the msys icon to open another shell
5.   In the opened terminal, type: fiber –h (or other command with –h)
Notices:
1, Pay attention to the space in the quoted command
2, you can try tar, tar --help, car --help in the opened shell, which will give you much more information (personally, I have not made them clear to me)
3, copy (or move) x3dna-dssr.exe, x3dna-snap.exe into C:\MinGW\msys\1.0\home\Administrator\x3dna-v2.3\bin though they can also be run with cmd(fig.dssr01)
By the way, you can get cmd by using windows+R or in the “start”, searching for it is OK.

Offline Maya12

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Re: How to install 3DNA on Windows?
« Reply #13 on: July 02, 2016, 11:53:13 am »
Dear MingyuSun,

Thank you for the reply.
Reinstalled and tried all the steps. The same problem is still there. I am not getting the Mcys icon on desktop.
Will try once again and inform you.



Offline Maya12

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Re: How to install 3DNA on Windows?
« Reply #14 on: July 02, 2016, 12:59:19 pm »
Thank you.
 All the three folders are in C: drive. When I am running x3dna_setup, one flash of window is coming. How it should come?
Maya


Thanks for your quick follow-up.

Where is 3DNA installed? What's the output of running the "x3dna_setup" Ruby script? There seems no shortcuts. Let's start from the very beginning for trace where the problem is.

Alternatively, you may want to install Cygwin which is closer to a Linux environment. A local expert with command-line skills would certainly be helpful.

Since this thread is becoming quite long, please start a new one. Based on this experience, I will consider to write a new "Howto" post with details on setting up 3DNA on Windows.

Best regards,

Xiang-Jun

 

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.