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Re: [scipion-users] localrec not present in scipion and what version of relion neede
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From: Pablo C. <pc...@cn...> - 2017-05-22 06:14:13
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Dear Dieter, you are almost there: after a: 1.- git clone https://github.com/I2PC/scipion.git 2.- cd scipion 3.- git checkout release-1.1 you should have release-1.1 code checked out. Then continue from here: step2-dependencies <https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies>. If you had previous version installed you will need to adjust configuration files, there are several way to do this, I'll explain the easiest, this is: 1.- Back up your *user config file*. From the console type: /mv ~/.config/scipion/scipion.conf ~/.config/scipion/scipion.conf.v1.0.backup/ 2.- Run /scipion config/ (this will regenerate you user config file compatible with release 1.1) 3.- run /scipion config --update/ (this will update your existing scipion_home config file with missing new variables) 4.- Review EM software folders name, at *<SCIPION_HOME>/software/em/*, this is the main change from release 1.0 to 1.1. Here you have 2 options: A) Simplest way would be to remove all folders there *except xmipp*. And install EM software needed again using scipion install <package-version>. Most of them are just a tar.gz extraction. It should be quick. And some versions have been updated like motioncor2. B) RenameEM packages folders (or create links) to match new naming convention (package-version). As an example, in release 1.0 the folder for frealign was named "frealign". Now, in release 1.1 it should have the version also in the name--> frealign-9.07 5.-Compile Xmipp with new code: /scipion install -j 5/ That should be all to install and migrate configuration from Scipion 1.0 to Scipion 1.1. Let us know how it goes and if you need any further assistance. All the best, Pablo. Scipion Team. On 19/05/17 17:24, Dieter Blaas wrote: > > 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...> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org <http://Slashdot.org>! >>>> http://sdm.link/slashdot >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> <mailto:sci...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> >>> >>> >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
