Re: [scipion-users] Scipion3 install question

[Grigory S. <sha...@gm...>]

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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On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer <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...> 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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