Re: [scipion-users] Scipion3 install question

[Teige Matthews-P. <tei...@gm...>]

That sounds probably right! On my install the module called scipion is found in …/scipion3/.scipion3env/bin/scipion , it and everything alongside it are owned by root and 755 permission and it works fine (I think it’s a venv install - at least I know I wanted to avoid miniconda).

Good luck
Teige

> On 3 Jun 2021, at 17:54, Grigory Sharov <sha...@gm...> wrote:
> 
> I think you should have a folder /usr/local/bin/scipion3/.venv/scipion3 where the venv is located..
> 
> Best regards,
> Grigory
> 
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
> 
> MRC Laboratory of Molecular Biology,
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> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
> 
> 
> On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer <tei...@gm... <mailto:tei...@gm...>> wrote:
> Hi Morgan,
> 
> I installed scipion3 and its packages a while ago and remember it was a bit tricky/fussy on Centos7 too.
> 
> Just some ideas, it seems like user’s python is not searching the directory where the scipion module is, or permissions stop it from finding the module?
> 
> The scipion launcher /usr/local/scipion3/scipion3 starts with the shebang #!/usr/bin/env python3, which should invoke the default python3 of the user’s environment. I don’t think this would be the issue, but maybe user has a different default python binary?
> 
> Or, you could use python -c ‘import sys; print(sys.path)’ to print out the directories where python will search for modules. Is it different between root and user?
> For me, it includes …/python3.8/site-packages , which contains scipioninstaller, and I think that eventually leads to it finding scipion3. I can’t tell exactly where the module referred to as “scipion” is located, but specifying its directory in PYTHONPATH could solve it?
> 
> Otherwise, potentially the directory where the scipion module is found has permissions that deny user access, and need chmod?
> 
> Hope it doesn’t take too many more knots before it’s working!
> Teige
> 
> 
>> On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im... <mailto:m....@im...>> wrote:
>> 
>> Dear all,
>> 
>> I wondered if anyone could help point me in the direction of installing scipion3 for all users on a machine (ultimately for cluster install for all users)? I seem to be tying myself in knots with what seems to be a trivial install.
>> 
>> As root, I am doing the following to install on Linux Mint 20 (after insuring all prequisite libraries are installed):
>> pip install scipion-installer
>> python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4
>> Then as user:
>> alias scipion3=/usr/local/bin/scipion3/scipion3 
>> scipion3
>> But I get an error:
>> 
>> /usr/bin/python: No module named scipion
>> (it runs ok for root)
>> 
>> It seems like this should just work, but after hours of playing around, I've had no success, and I cannot find anything on multiuser installs on linux.
>> 
>> thanks,
>> 
>> Morgan
>> 
>> 
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