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

[#CHEW B. L. A. <CHEW0357@e.ntu.edu.sg>]

Dear Pablo,


Thank you! Changing the scipion3 launcher works!


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

Best Regards

Alvin CHEW | Ph.D. Student | Lee Kong Chian School of Medicine | NTU Institute for Health Technologies (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>~

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents.


________________________________
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
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.



Best Regards



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>~







_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users


--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team