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

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

Great! Thanks for confirming it.


On 24/11/21 9:27, #CHEW BING LIANG ALVIN# wrote:
> Dear Pablo,
>
> Thank you! Changing the scipion3 launcher works!
>
>
> os.environ["PATH"] = 
> ":".join(["/home/dlsw1/anaconda/envs/scipion3/bin", 
> os.environ.get("PATH", "")])
>
>
> BestRegards
>
> Alvin CHEW | Ph.D. Student |Lee Kong Chian School of Medicine | NTU 
> Institute for HealthTechnologies (HealthTech NTU), Interdisciplinary 
> Graduate Programme| Nanyang Technological University | 59 Nanyang 
> Drive, Experimental Medicine Building, 03-07-01, Singapore 636921Tel: 
> (65) 6592-3990 GMT+8h| Email: chew0357@e.ntu.edu.sg | Web: 
> http://www.lkcmedicine.ntu.edu.sg <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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> ------------------------------------------------------------------------
> *From:* Pablo Conesa <pc...@cn...>
> *Sent:* Wednesday, October 27, 2021 4:51 PM
> *To:* sci...@li... 
> <sci...@li...>
> *Subject:* Re: [scipion-users] [Troubleshooting request] Error opening 
> scipion3 after topaz installation
>
> 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*
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*