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Author Topic: Problem running x3DNA on Cygwin  (Read 5098 times)

Offline Hector86

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Problem running x3DNA on Cygwin
« on: September 04, 2015, 05:09:54 am »
Hello!

I have installed x3DNA on Cygwin correctly, but everytime I close Cygwin, x3DNA seems to be uninstalled and x3DNA commands are not recognized until I reinstall it. This is the only software in which I have experienced this iisues on Cygwin.

Thanks in advance.

Offline xiangjun

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Re: Problem running x3DNA on Cygwin
« Reply #1 on: September 04, 2015, 10:36:15 am »
Thanks for using 3DNA and for posting your question on the Forum.

What you experienced is certainly unexpected, and has never been reported previously. For verification, I've just installed x3dna-v2.2-cygwin-win.tar.gz on Cygwin in Win7, installed and set up 3DNA, ran find_pair, closed Cygwin. When I then opened a Cygwin terminal again, everything of the 3DNA v2.2 distribution is still there and works, as it should be.

Could you provide more details about your situation? With screenshots probably.

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

Offline Hector86

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Re: Problem running x3DNA on Cygwin
« Reply #2 on: September 07, 2015, 06:25:11 am »
Here is the installation procedure I have followed to install X3DNA, the last image is what I get when I close Cygwin terminal and I open it again executing find_pair -h.
I can reinstall the program everytime by simply typing the "export" commands again from whatever location, but if I close Cygwin again, x3dna is uninstalled again.








Offline xiangjun

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Re: Problem running x3DNA on Cygwin
« Reply #3 on: September 07, 2015, 02:32:34 pm »
Thanks for providing further details. The screenshots certainly help in identifying where the problem really is.

Quote
I can reinstall the program everytime by simply typing the "export" commands again from whatever location, but if I close Cygwin again, x3dna is uninstalled again.

3DNA is not uninstalled at all. It is just that the settings for the X3DNA environmental variable and command PATH are lost each time you exit from Cygwin. Your Cygwin installation seems weird -- you are under the raw /cygdrive/c folder notation. Normally, when you open a Cygwin terminal, you get to a Linux/Unix-like directory, such as /home/xiangjun.

The instruction from running the x3dna_setup script is as follows:

Quote
  (3) ./x3dna_setup
          to run X3DNA, you first need to do two things:
              o set up the X3DNA environment variable
              o add $X3DNA/bin to your command search path
          for your 'bash' shell, add the following into ~/.bashrc:
          --------------------------------------------------------------
              export X3DNA='/home/xiangjun/x3dna-v2.2'
              export PATH='/home/xiangjun/x3dna-v2.2/bin':$PATH
          --------------------------------------------------------------
          and then run: source ~/.bashrc

Did you notice the error message when you ran the command: "source ~/.bashrc". Somehow, you do not have .bashrc under the home directory of your Cygwin installation. Since you did not add the two "export" lines into ~/.bashrc, so you need to run the two exports each time. In any event, the x3dna-v2.2 folder is still there, certainly not 'uninstalled'.

It'd help to investigate your Cygwin installation, perhaps with help from a local experienced Linux/Cygwin user. Specifically, please open a Cygwin terminal, and type the following commands:

Code: [Select]
pwd
cd
pwd

What do you get? Again, please use screenshots.

With your current settings, the following instructions may help:

Code: [Select]
touch ~/.bashrc
echo "export X3DNA='/cygdrive/c/X3DNA/x3dna-v2.2'" >> ~/.bashrc
echo "export PATH='/cygdrive/c/X3DNA/x3dna-v2.2/bin':$PATH" >> ~/.bashrc

Please have a try and report back how it goes.

Xiang-Jun
« Last Edit: September 07, 2015, 02:41:15 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Hector86

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Re: Problem running x3DNA on Cygwin
« Reply #4 on: September 08, 2015, 06:55:02 am »
Thanks for your quick answer.

My fault, I was installing x3dna outside my home directory on purpose, my home directory is"/cygdrive/c/Users/Héctor" (see first picture below). There is a  .bashrc file in that directory, indeed.

I have tried to install x3dna on that directory and when I type "source ~/.bashrc" I have got the output of the second picture and then same issues when closing Cygwin terminal.

I have also tried the "touch" and "echo" commands on my current settings without any result.




Offline xiangjun

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Re: Problem running x3DNA on Cygwin
« Reply #5 on: September 08, 2015, 10:03:12 am »
Thanks for posting back with screenshots.

In the default Cygwin terminal, my home directory shows up as /home/xiangjun. Yours is more complicated. This just looks strange to me, and may not be the real issue.

The real problem is that your ~/.bashrc is not set up correctly. Please pay attention to the first line of running source ~/.bashrc. I do not know Spanish, but there seems to be syntax error near (. Moreover, the settings for X3DNA in the ~/.bashrc file no longer match its current installation.

Your settings shown previously are directly under "/cygdrive/c/X3DNA/x3dna-v2.2", and my suggestion emphasized in bold in my previous reply is based on that info. In the new screenshots, you seems to have installed 3DNA under your home directory "/cygdrive/c/Users/Héctor/x3dna-v2.2". You need to fix the error in your ~/.bashrc file, and updated the X3DNA environment variable and path there accordingly.

Setting up 3DNA is a straightforward process, and should take no more than a couple of minutes. First is the X3DNA environment variable, telling where 3DNA is installed. Second is to add the $X3DNA/bin directory to your command path so that 3DNA binaries can be executed anywhere. These two steps are facilitated by the x3dna_setup script which makes installation-specific suggestions.

Before you can get your ~/.bashrc file fixed, the only other thing I can suggest to get 3DNA up and running is as below:
# Now matter where you have installed 3DNA, change to its bin/ directory
./x3dna_setup
# Create a text file named 'config-3dna' under your home directory
#   and add the two export lines from above x3dna_setup output into 'config-3dna'
# Then you can just run the following command
source ~/config-3dna

If you have difficulty to understand and follow the above procedure, your best bet is to ask for help from a local expert.

HTH,

Xiang-Jun
« Last Edit: September 08, 2015, 10:05:51 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Hector86

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Re: Problem running x3DNA on Cygwin
« Reply #6 on: September 09, 2015, 10:42:54 am »
I have tried your last advice and it did not work. I have also installed x3dna on 64 bit Cygwin and on Ubuntu with same issues. I agree with you that the problem is due to .bashrc.

I will report here if I solve the issues.

Thanks.

Offline xiangjun

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Re: Problem running x3DNA on Cygwin
« Reply #7 on: September 09, 2015, 11:02:08 am »
Thanks for reporting back the 3DNA setting up issue you still face. I am curious to see this through:

Quote
I have also installed x3dna ... on Ubuntu with same issues. I agree with you that the problem is due to .bashrc

Please do the following on your 3DNA Ubuntu installation.

Code: [Select]
echo $SHELL
x3dna_setup
   # report the output of the above 3DNA setup script.
   # add the two "export" from the above script to ~/.bashrc using a text editor
cat ~/.bashrc

If the instruction from the setup script is followed faithfully, you should be able to get 3DNA up and running with out a problem. At the very least, it will show where things go wrong.

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 xiangjun

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Re: Problem running x3DNA on Cygwin
« Reply #8 on: September 09, 2015, 11:59:40 am »
Just for the record, here is the email I just sent out:

Quote
Hi,

Thanks for using 3DNA. I am sorry for your frustrating experience to get 3DNA up and running. Your case represents a worst-case scenario in my support of 3DNA well over a decade. If we can solve your problem, that'd be helpful for other potential 3DNA users who are not experienced with the command line environment.

If you use Skype, I am willing to chat with you. With screen-sharing, it is an effective to solve the issue quickly.

Please let me know.

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

Offline Hector86

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Re: Problem running x3DNA on Cygwin
« Reply #9 on: September 10, 2015, 05:01:02 am »
Hi again!

Done! I have installed X3DNA on Ubuntu perfectly, the only step I have changed is the installation verification in which I wrote "./find_pair -h" instead of "find_pair -h" and (I do not why) it worked this time. The Ubuntu .bashrc file contains the 2 export commands at the end.

I have manually modified the .bashrc file on Cygwin by adding the two export lines, and this time it is working perfectly.

So the issues are fixed, thank you so much for your kind attention.

Just a little offtopic: I can´t have access to w3dna.rutgers.edu these days, (Forbidden access issue appears), I do not know if the issue is related to the webpage or to my University IP adress.

Thanks for everything again.

Offline xiangjun

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Re: Problem running x3DNA on Cygwin
« Reply #10 on: September 10, 2015, 08:04:20 am »
Thanks for posting back the good news. Persistence wins!

Quote
Just a little offtopic: I can´t have access to w3dna.rutgers.edu these days, (Forbidden access issue appears), I do not know if the issue is related to the webpage or to my University IP adress.

This is certainly not out of topic. As shown in clearly in the w3DNA section on the 3DNA Forum, and the screenshot below for the record,



It is the Dr. Olson lab at Rutgers that takes the credit and responsibility for maintaining the w3dna.rutgers.edu (interfaced with 3DNA v2.0, dated 2009) website. Yet, past experience and the current status have shown unambiguously things are not working satisfactorily.

After many frustrations in dealing with Rutgers on this presumably simple issue, I've made up my mind to create a new simple web interface to 3DNA v2.2 that will be in sync with any future distribution. I aim to get a working site by next week, and I will make an announcement when it is ready. Time to move on, and leave w3dna.rutgers.edu behind.

Best regards,

Xiang-Jun
« Last Edit: September 10, 2015, 08:07:27 am by xiangjun »
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]· 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.