Re: [scipion-users] Scipion3 install question

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

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
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>>
>>     ~ ~ ~
>>
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>>
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>>
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