Re: [scipion-users] Scipion3 install question

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

Soz for spam - think I’m wrong to say …/scipion3/.scipion3env/bin/scipion is the module, I think it’s rather in scipion3/.scipion3env/lib/python3.6/site-packages/scipion/
I guess that if users are denied permission to any of this, then it will fail to load the module.

Open question: is it OK generally to do chmod -R 755 to the whole scipion directory - and maybe it solves the problem Morgan has?

> On 3 Jun 2021, at 18:14, Teige Matthews-Palmer <tei...@gm...> wrote:
> 
> 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... <mailto: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,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> 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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>>> Department of Life Sciences
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>>> Imperial College London
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