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Author Topic: Mac OSX Compilation Difficulty  (Read 2372 times)

Offline rwmolt

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Mac OSX Compilation Difficulty
« on: January 18, 2016, 11:13:02 pm »
Hi,

I am currently on OSX v. 10.11.2. I followed the directions for compiling said software up to the point of sourcing my profile and encountered a difficulty. Specifically, the following commands went just fine:

tar pzxvf x3dna-v2.1-linux-64bit yada yada yada
cd x3dna_v2.1/bin
./x3dna_setp
setenv X3DNA '/home/xiangjun/x3dna-v2.1'
setenv PATH '/home/xiangjun/x3dna-v2.1/bin':$PATH

I do not seem to have a .cshrc file, such that I cannot
source ~/.cshrc
without getting the error
/Users/robertmolt/.cshrc: No such file or directory.

I cannot do the next command, either, perhaps as a result:
find_pair -h

I would be appreciative of any advice that can be given to compile from this point forward. I apologize if this is an elementary Linux question.



Offline xiangjun

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Re: Mac OSX Compilation Difficulty
« Reply #1 on: January 19, 2016, 12:13:16 am »
Hi,

Thanks for using 3DNA, and for posting your setup question on the Forum.

From the subject line, I assume you are on Mac OS X (even though the procedure should be the same for Linux). You've run the x3dna_setup script successfully. You did not paste the full output from running the setup script. However, from the two lines of output (setenv), you are most likely using a csh/tcsh shell (even though this is a bit weird since the Mac OS X and Linux operating systems I am aware of normally have bash shell by default).

Could you please conform the followings?

Code: [Select]
echo $SHELLIs it csh or tcsh?

Code: [Select]
ls ~/.tcshrcDo you have a .tcshrc file instead?

In any event, you are close to get 3DNA up and running. For the current terminal window, you can simply copy and paste the two 'setenv' lines, and then 'find_pair -h' should work.

Please post back how it goes. I am here to getting you through the process.

Xiang-Jun


PS. Presumably, getting 3DNA up and running should be straightforward, with the minimum setting of two environment variables, which itself is automated by the x3dna_setup script. However, I've learned through experimence that for new Linux/Mac OS X users, the command-line setting process could be a hassle. That's one of the reasons I've made DSSR and SNAP completely self-contained to eliminate the setup step.

« Last Edit: January 19, 2016, 12:23:56 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline shoara

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Re: Mac OSX Compilation Difficulty
« Reply #2 on: May 10, 2016, 02:23:34 pm »
Hello,

I was able to download the folder x3dna-v2.1 to my Mac OS 10.11.4, but I don't know how to instal the program and get 3D structures of my DNA aptamer. Can anybody help please?

Thanks,
A.

Offline xiangjun

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Re: Mac OSX Compilation Difficulty
« Reply #3 on: May 10, 2016, 02:31:47 pm »
Please use the latest 3DNA v2.3 instead, and report back any problem you may have.

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

Offline shoara

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Re: Mac OSX Compilation Difficulty
« Reply #4 on: May 10, 2016, 02:41:14 pm »
Hi,
Thank you for your prompt reply.
When I extract the zipped file, I only get the x3dna-v2.3 folder which has 8 sub-folders (bin, config, doc, examples, fiber, lib, np_recipes, and perl_scripts). None of the files seem to run under Mac. Can you please instruct me how continue after I extracted the folder?

Thanks.

Offline xiangjun

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Re: Mac OSX Compilation Difficulty
« Reply #5 on: May 10, 2016, 02:50:06 pm »
Did you see the link on how to set up 3DNA in the download page? You may also check the doc/ directory and follow instructions over there.

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

Offline shoara

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Re: Mac OSX Compilation Difficulty
« Reply #6 on: May 10, 2016, 03:01:45 pm »
Yes, I saw the instructions on Download page. I only found instructions for Linux and Windows. How do they differ from Mac OX though?

Offline xiangjun

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Re: Mac OSX Compilation Difficulty
« Reply #7 on: May 10, 2016, 03:21:46 pm »
You follow the instructions in the Linux section. In fact, I've just revised the section title to include Mac OS X. Please let me know how things can be made clearer.

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]· 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.