Re: [scipion-users] Sphire plugin installation & running

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

I was able to run sphire plugin 1.4.0 and cryolo 1.6.1 in scipion 2 now
with no errors. I ran training with fine tuning of either general or input
model and got no errors with json config file.
Unless /usr/local/bin/startEMAN2scipion does something weird I don't see
any other solutions.


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 Tue, Jun 9, 2020 at 3:41 PM Dmitry Semchonok <Sem...@gm...> wrote:

> Dear Grigory,
>
> Thank you!
>
> Yes, the file is there.
>
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
> On 9. Jun 2020, at 16:24, Grigory Sharov <sha...@gm...> wrote:
>
> Hi Dmitry,
>
> Though I am not the maintainer of the sphire plugin and unfortunately I
> don't have scipion 2.0 at the moment, I couldn't reproduce this with the
> newer release of cryolo / scipion 3. Installation error you have can be
> ignored afaik, since you cant fix it without updating the cryolo binary.
> The run error you have says missing config.json file. Can you check if this
> file is missing in the extra folder of the protocol run?
>
> 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 Tue, Jun 9, 2020 at 1:35 PM Dmitry Semchonok <Sem...@gm...>
> wrote:
>
>>
>>
>>
>>
>> Dear Grigory,
>>
>> We followed your suggestions to make the sphire work.
>>
>> The problem appeared to be in the initial sphire plugin installation.
>> So we decided to re-install the sphire.
>>
>> During installation we got the error - please see the files attached.
>>
>> Could you please suggest how could we fix it?
>>
>>
>>
>>
>> Thank you!
>>
>> Sincerely,
>> Dmitry
>>
>>
>>
>