Re: [scipion-users] How to export files?

[Jose M. de la R. T. <del...@gm...>]

Hi Matt,

Just one clarification...what Gregory mention about 'export protocols' is
related to exporting some of the jobs executing in Scipion as ready-to-use
files for importing into orther programs (mainly Relion right now).

If I understood correctly your question, you are talking more about
transferring the data of a pre-processing project. Scipion projects are
self-contained folders (except for initial import that are symbolic links
that can be broken...and restored). So, it is up to each facility how to
manage the Scipion data generated for one session. In our case in
Stockholm, we store the raw files and the pre-processing project for one
month. During that time, users are responsible for connecting to our server
and copy the data back. We remove session data that is more than one month
older.

Managing data transfer/policies is beyond the scope of Scipion...and it is
almost impossible to do it in a general (and robust) way that serve all the
different situations.

Hope this helps,
Best,
Jose Miguel




On Fri, May 24, 2019 at 5:36 PM Gregory Sharov <sha...@gm...>
wrote:

> Hello Matt,
>
> Thank you for your interest! At the moment there are two protocols (relion
> - export ctf and relion - export particles) that can create a star file for
> importing into Relion. You can find them by using Ctrl+F, it's true they
> are not in export section at the moment (to be fixed).
> If you also want to move the data files outside the project you will have
> to fix the produced star file (awk can do it neatly).
>
> The processed data is kept unless you overwrite/delete the project.
> Unless, of course, if you plan to remove the old scipion projects as soon
> as the session if finished.
>
> Hope this helps,
> 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 <+44%201223%20267542>
> e-mail: gs...@mr...
>
>
> On Fri, May 24, 2019 at 4:24 PM Matt Harrington <ma...@ms...> wrote:
>
>>
>> We're evaluating Scipion for use by our facility, not necessarily for use
>> by individual users.  I recently had a demo and was left with one
>> question.  It's not clear how to export processed data to final
>> destination.  We have a simple pipeline of Import -> MotionCor2 ->
>> Ctffind.  It appears that processed files are left in the Scipion working
>> directory.  I'm told that previously processed data will be deleted when a
>> new user starts collecting and starts a new Scipion run.
>>
>> The "Protocols SPA" view has a section titled "Export", but it doesn't
>> appear to list any plugins.
>>
>> Is my understanding correct?  How should we proceed?
>>
>> Matt
>>
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