Re: [scipion-users] Scipion3 install question

[Morgan B. <m....@im...>]

Hi Teige, Grigory, Pablo,

Many thanks for helping me untie myself.

Turns out the key was Teige's astute observation: I have multiple Python 
installs (not for the first time...), and root was referencing a 
different install to standard users. Fixing that and it all worked nicely.

I then enabled all users to install (and, therefore, break...) scipion 
modules.

All seems to work a treat now. Thanks again, all.

Morgan



On 03/06/2021 10:18, Pablo Conesa wrote:
>
> All seems to be around what Grigory and Teige are saying.
>
> I'm curious about what is going on there and learn how to do that 
> setup with virtualenv.
>
> If you like, I'm available for a shared desktop session to find out, 
> and later document how to do that setup.
>
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> On 3/6/21 10:54, Grigory Sharov 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
>>>
>>>
>>>     -- 
>>>     Dr Morgan Beeby
>>>     Department of Life Sciences
>>>     c/o Department of Chemistry Stores
>>>     Imperial College London
>>>     Frankland Road
>>>     London, SW7 2AZ
>>>     United Kingdom
>>>
>>>     Office: +44 (0)20 7594 5251
>>>     Web : www.beebylab.org
>>>
>>>     ~ ~ ~
>>>
>>>     Schedule a meeting with me: https://go.oncehub.com/MorganBeeby
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-- 
Dr Morgan Beeby
Department of Life Sciences
c/o Department of Chemistry Stores
Imperial College London
Frankland Road
London, SW7 2AZ
United Kingdom

Office: +44 (0)20 7594 5251
Web : www.beebylab.org <www.beebylab.org>

~ ~ ~

Schedule a meeting with me: https://go.oncehub.com/MorganBeeby 
<https://go.oncehub.com/MorganBeeby>

~ ~ ~

Drop in office hours, no appointment necessary, over the next 7 days:

(Teams link 
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