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Re: [scipion-users] localrec not present in scipion and what version of relion neede
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From: Dieter B. <die...@me...> - 2017-05-19 15:24:49
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Hi Juha, Miguel & all,
please forgive me my ignorance but what is the command for
installing scipion *release-1.1?* Can it be installed via git clone or
do I have to use the tar.gz file? I cannot find the correct name in github!
Dieter*
*
*
*
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: die...@me...
------------------------------------------------------------------------
Am 19.05.2017 um 08:40 schrieb Dieter Blaas:
>
> Dear all,
>
> thank you very much for these explanations, I shall do as suggested!
>
> Best wishes, Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail:die...@me...
> ------------------------------------------------------------------------
> Am 19.05.2017 um 08:11 schrieb Juha Huiskonen:
>> Dear Dieter,
>>
>> I just checked and Jose Miguel is right, when run localrec from
>> Scipion, localrec needs to have Relion 1.4 present. So when you
>> install Scipion, please install both. However, 1.4 is used only
>> internally for some functions - you can still classify, refine and
>> reconstruct the sub-paricles in Relion 2.0.
>>
>> Please double check that you have this line in your
>> .config/scipion/scipion.conf file:
>> LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4
>>
>> Best wishes,
>> Juha
>>
>>
>> On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin
>> <del...@gm... <mailto:del...@gm...>> wrote:
>>
>> Dear Dieter,
>>
>> As Juha suggested, it would be better to use branch release-1.1,
>> which is going to be the next official release.
>>
>> Juha, correct me if I'm wrong, but I think that localrec would
>> need Relion 1.4, and currently does not work with 2.0. In
>> Scipion, both versions can live together. Indeed, you don't need
>> to modify your environment, Scipion will do it for you when
>> launching Relion jobs (the same for other packages). It is also
>> possible to reuse package installations (if the version is the
>> one used in Scipion). You just need to create a symbolic link in
>> the scipion/software/em folder with the proper name
>> (package-version).
>>
>> Cheers,
>> Jose Miguel
>>
>>
>> On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen
>> <ju...@st... <mailto:ju...@st...>> wrote:
>>
>> Dear Dieter
>>
>> Please update your Scipion to 1.1 beta (balbino) from github
>> branch release-1.1-fixes. Localrec is part of that version
>> and will be in the official release 1.1 when that comes out.
>> It is also compatible with Relion 2.0.
>>
>> Best wishes,
>> Juha
>>
>> On 19 May 2017, at 08:14, Dieter Blaas
>> <die...@me...
>> <mailto:die...@me...>> wrote:
>>
>>> Dear colleagues,
>>>
>>> I tried to install localrec in scipion (Scipion v1.0.1
>>> (2016-06-30) Augusto) following this instruction:
>>> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install
>>> <https://github.com/OPIC-Oxford/localrec/wiki/How-to-install>
>>> but 'scipion
>>> --help' does not show this software and 'scipion install
>>> localrec' does
>>> not find it.
>>>
>>> 1) how do I install localrec?
>>>
>>> 2) once installed will it run also by using the latest
>>> relion version
>>> (i.e. relion-2.0.x, which I have as a separate and
>>> independent install)
>>> or do I have to use the old relion (v-1.4) and if so, can
>>> both version
>>> live side by side (for example relion-1.4 within scipion and
>>> relion-2.0.5 outside scipion?
>>>
>>> Thanks a lot for hints,
>>>
>>> Dieter
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> Dieter Blaas,
>>> Max F. Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Fax: 0043 1 4277 9616,
>>> e-mail: die...@me...
>>> <mailto:die...@me...>
>>> ------------------------------------------------------------------------
>>>
>>>
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>
>
>
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