Re: [scipion-users] Problem with Scipion and Xmipp

[David M. <dma...@cn...>]

Great to hear it's fixed now!

We are working to make this more intuitive in the next version.

Thanks to you for reporting.


Cheers!

<http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@cn... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

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On Tue, Jan 21, 2020 at 9:56 AM Dario Saczko-Brack <
dar...@go...> wrote:

> Hi David,
>
> that was the "trick". I have installed the plugin, without going back to
> the plugin manager, expanding scipion-em-xmipp and install one of the
> binary. Now it seems to work, at least there is no error message upon
> startup. The tests including xmipp-procedures also pass without error.
> Thanks again.
>
> Also thank You Wolfgang and Grigory forthe support.
>
> Best
>
> Dario
>
>
> On 20.01.20 21:36, David Maluenda wrote:
>
> Hi Dario and Scipion-Users,
>
> It seems that Xmipp plugin is installed but not the software below. Once
> the Xmipp plugin is installed, the Xmipp software appears below the Xmipp
> plugin in the plugin manager. You should choose a binary (for Centos or For
> Debian distros) o the sources to complie (other distros). More informarion
> can be found in the link that Gregory placed.
>
>
> Thanks!
>
> _____
> Dr. David Maluenda Niubó
> 619.029.310 - dma...@cn...
> Centro Nacional de Biotecnología - CSIC
> BioComputing Unit
>
> El lun., 20 ene. 2020 17:45, Grigory Sharov <sha...@gm...>
> escribió:
>
>> Hi Dario,
>>
>> It may as well be that xmipp installation through Plugin manager has
>> failed, you should check the Plugin.err or log file for details. If that's
>> the case you might try to install xmipp
>> <https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#step-4-installing-xmipp3-and-other-em-plugins>
>> from command line.
>>
>> 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 <+44%201223%20267228>
>> e-mail: gs...@mr...
>>
>>
>> On Mon, Jan 20, 2020 at 4:37 PM Lugmayr, Wolfgang <w.l...@uk...>
>> wrote:
>>
>>> hi,
>>>
>>> i extended the original scipion.conf with some site information and call
>>> it like:
>>> scipion --config scipion_cssb.conf
>>>
>>> the package section below for example is not in the original scipion.conf
>>>
>>> [PACKAGES]
>>> EM_ROOT = software/em
>>> MOTIONCOR2_BIN = MotionCor2_1.2.6-Cuda101
>>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda-10.1/lib64
>>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.2.6
>>> XMIPP_HOME = %(EM_ROOT)s/xmipp
>>>
>>> maybe this helps?
>>>
>>> cheers,
>>> wolfgang
>>>
>>>
>>>
>>> ----- Original Message -----
>>> From: "Mailing list for Scipion users" <
>>> sci...@li...>
>>> To: "Mailing list for Scipion users" <
>>> sci...@li...>
>>> Cc: "Dario Saczko-Brack" <dar...@go...>
>>> Sent: Monday, 20 January, 2020 16:57:23
>>> Subject: [scipion-users] Problem with Scipion and Xmipp
>>>
>>> Hi all,
>>>
>>> I have a question about the xmipp within scipion, as it seems not to
>>> work properly on my machine. I always get the error message upon the
>>> scipion start, although I have installed xmipp using the plugin manager
>>> (and already several times removed+installed again):
>>>
>>> >  >>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
>>> >   > Please install Xmipp to get full functionality.
>>> > (Configuration->Plugins->scipion-em-xmipp in Scipion manager window)
>>>
>>>
>>> Does anyone had this problem too and knows how to deal with it? If there
>>> are any more information you need, let me know.
>>>
>>>
>>> Thanks in advance
>>>
>>> Dario
>>>
>>>
>>>
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>>>
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