Re: [scipion-users] [Troubleshooting request] Error opening scipion3 after topaz installation

[Pablo C. <pc...@cn...>]

I think the problem resides in the last image.


You are adding topaz's python to the PATH making it the default python 
and that one is taking priority over other pythons, even when activating 
environments


Can you make a quick test?


1.- Comment the line in your bash.rc where you are addig topaz to the 
PATH variable.

2.- Close the terminal and open it again (or source your bash.rc)

3.- Try to run Scipion3


Alternatively, you might want to modify scipion3 launcher adding a line 
to prioritize scipion python?


os.environ["PATH"] = ":".join(["/home/dlsw1/anaconda/envs/scipion3/bin", 
os.environ.get("PATH", "")])


Haven't tried it.


On 27/10/21 5:00, #CHEW BING LIANG ALVIN# wrote:
> Dear Scipion community,
>
> I had no issues using scipion3 until I have installed topaz under the 
> installation instructions listed in cryosparc 
> https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz 
> <https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz>
> I have tried reading through the troubleshooting guide but could not 
> seem to find a solution to my problem here.
> I have attached various screenshots that show the path pointed out by 
> "scipion3" command points to topaz, but this is not the case in my 
> bashrc setting. Screenshots *_1 and *_2 are the list of documents in 
> the Programme and anaconda env.
> I could not seem to find the scipion.conf file as well, I am unsure if 
> setting the scipion.conf is the fix I need in my case or simply 
> reinstall scipion3 by following the installation guide again?
>
> Thank you and hope to receive any useful advice on how to proceed.
>
> BestRegards
>
> Alvin CHEW | Ph.D. Student |Nanyang Technological University 
> |<http://www.lkcmedicine.ntu.edu.sg/>
>
> /"(You) who (have) a why to live can bear almost any how.//"/
> ~Friedrich Nietzsche 
> <http://www.brainyquote.com/quotes/quotes/f/friedrichn103819.html>~
>
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*