Re: [scipion-users] Problems with scipion installation

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

Hi Bruno,

it does look like you still using system python
(/usr/lib/python2.7/subprocess.py) and not the scipion one. How do you
launch scipion?

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 267542
e-mail: gs...@mr...


On Thu, Jun 28, 2018 at 1:48 PM Bruno Matsuyama <bru...@gm...>
wrote:

> Hi Gregory,
>
> I just tried that, but didn't work. The same error message keeps appearing.
>
> Traceback (most recent call last):
>   File "./scipion", line 34, in <module>
>     import subprocess
>   File "/usr/lib/python2.7/subprocess.py", line 72, in <module>
>     import select
> ImportError: No module named select
>
> Best Regards,
>
> Bruno
>
>
>
> On Tue, 26 Jun 2018 at 18:48, Gregory Sharov <sha...@gm...>
> wrote:
>
>> Hello Bruno,
>>
>> I might be wrong, but a wild guess:do you have anything sourced like
>> eman2 which might setting its own PYTHONPATH?
>>  Did you try to change first line in the main ./scipion file to point it
>> to the python provided with scipion? (software/bin/python)
>>
>>
>> On Tue, Jun 26, 2018, 20:01 Bruno Matsuyama <bru...@gm...>
>> wrote:
>>
>>> I searched on the internet and tried some things, but still not work.
>>> What I found is differences between how the modules are called in the
>>> script, but I am not sure if I am worsening the situation, because I dont
>>> have much experience with ubuntu os.
>>>
>>> Best Regards,
>>>
>>> Bruno
>>>
>>> On Tue, 26 Jun 2018 at 14:56, Patrick Goetz <pg...@ma...>
>>> wrote:
>>>
>>>> The default python on Ubuntu 18.04 seems to still be 2.7:
>>>>
>>>> cnsit@rossmann:/usr/bin$ cat /etc/lsb-release
>>>> DISTRIB_ID=Ubuntu
>>>> DISTRIB_RELEASE=18.04
>>>> DISTRIB_CODENAME=bionic
>>>> DISTRIB_DESCRIPTION="Ubuntu 18.04 LTS"
>>>> cnsit@rossmann:/usr/bin$ ls -l python
>>>> lrwxrwxrwx 1 root root 9 May  8 12:15 python -> python2.7
>>>>
>>>>
>>>> On 06/25/2018 05:44 PM, Jose Miguel de la Rosa Trevin wrote:
>>>> > Hi Bruno,
>>>> >
>>>> > Maybe Ubuntu 18 comes with Python 3 by default? Although we have
>>>> tested
>>>> > the install with it.
>>>> > Did you search about this error in Ubuntu? Just in case could give us
>>>> > some hint.
>>>> >
>>>> > Best,
>>>> > Jose Miguel
>>>> >
>>>> >
>>>> > On Mon, Jun 25, 2018 at 10:04 PM Bruno Matsuyama
>>>> > <bru...@gm... <mailto:bru...@gm...>> wrote:
>>>> >
>>>> >     Hello,
>>>> >
>>>> >     I'm having some trouble to install scipion  and I hope that
>>>> somebody
>>>> >     here can help me. I'm using Ubuntu 18.04, and after installing the
>>>> >     dependencies, when I tried to generate the configuration files, I
>>>> >     get the following message:
>>>> >
>>>> >       ./scipion config
>>>> >
>>>> >     Traceback (most recent call last):
>>>> >        File "./scipion", line 34, in <module>
>>>> >          import subprocess
>>>> >        File "/usr/lib/python2.7/subprocess.py", line 72, in <module>
>>>> >          import select
>>>> >     ImportError: No module named select
>>>> >
>>>> >     Did someone had the same error or know how to fix it ?
>>>> >
>>>> >     Best Regards,
>>>> >
>>>> >     Bruno
>>>> >
>>>> >
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