Menu
▾
▴
Re: [scipion-users] Can't import particles from relion
|
From: Grigory S. <sha...@gm...> - 2020-11-18 16:31:18
|
Hi Stephan,
It looks like a problem with the plugin installation. Can you try:
scipion3 uninstallp -p scipion-em-relion
scipion3 installp -p scipion-em-relion --noBin
and then re-run import particles?
PS. The plugin version (3.0.0.b7) is independent from the Relion binaries
version (3.1.0).
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 Wed, Nov 18, 2020 at 4:03 PM Tetter Stephan <tet...@or...>
wrote:
> Dear all,
>
>
> I have freshly installed Scipion3. When I wanted to import particles from
> a refinement done in relion3.0, I got an error message. I didn't have
> Relion installed on the same computer as the Scipion installation, so that
> sounded reasonable. Thus, I've installed Relion 3.1 manually. Still
> couldn't import the particles. I've tried to install Relion via the Scipion
> plugin manager, and everything went well. I've installed relion without the
> GUI, but I assume that shouldn't be an issue. The installation should be
> fine:
>
>
> $ relion_image_handler --version
> RELION version: 3.1.1-commit-9f3bf1
> Precision: BASE=double
>
> Again, I've tried to import the particles in Scipion, but it still doesn't
> work:
>
> ########################
>
> Protocol validation failed. It usually happens because there are some
> input missing. Please check if the error message gives you any hint:
> Error: Exception
> Description:
>
> > error when importing from relion: No module named 'relion.convert'.
> Relion is needed to import .star files
> File "<frozen importlib._bootstrap>", line 991, in findand_load
> Check the plugin manager (Configuration->Plugins in Scipion manager
> window)
> or use 'scipion installp --help --checkUpdates' in the command line to
> check for upgrades,
> it could be a versions compatibility issue.
>
> Traceback:
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1878, in validate
> childErrors = self._validate()
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_import/particles.py",
> line 245, in validate
> ci = self.getImportClass()
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocolimport/particles.py",
> line 176, in getImportClass
> RelionImport = Domain.importFromPlugin('relion.convert',
> 'RelionImport',
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py",
> line 294, in importFromPlugin
> output = _tryImportFromPlugin(objects)
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py",
> line 291, in tryImportFromPlugin
> Domain._pluginNotFound(plugName, errMsg, doRaise)
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py",
> line 437, in __pluginNotFound
> raise Exception("\n\n" + raiseMsg)
>
> ##############################
>
> Checking for updates as instructed in the error messages gives the
> following. Curiously, this points to a Relion3.0 installation.
>
> ##############################
>
> $ ./scipion3 installp --help --checkUpdates
> Scipion v3.0.6 - Eugenius
> WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined.
> Relying on conda being in the PATH
> Warning: Couldn't get remote plugin data for scipion-em-deepfinder
> Warning: Couldn't get remote plugin data for scipion-em-tomoj
> WARNING: scipion-ed-dials's release 3.0.1a2 did not specify a compatible
> Scipion version. Please, remove this release from pypi
> WARNING: scipion-ed-dials's release 3.0.1a3 did not specify a compatible
> Scipion version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.0 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.0a2 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.1 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.1a2 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 3.0.1a2 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> usage: scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
>
> optional arguments:
> -h, --help show help
> --noBin Optional flag to install plugins only as a python
> module,
> without installing the plugin binaries. This will
> affect
> all plugins specified in the command.
> --checkUpdates Optional flag to check which plugins have new
> releases.
> -p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion
> ...]
> - pluginName: the name of the plugin to
> install from the list
> of available plugins shown below.
> - pluginVersion: (optional) pip version to
> install. If not specified,
> will install the latest
> compatible with current Scipion.
> --devel Optional flag to indicate that we will pass
> install sources instead
> of pip names. Sources might be local paths or git
> urls. With local
> paths, will do pip install -e (editable mode). It
> is expected to find
> the plugin name in the basename of the path or in
> the repo name.
> (i.e. it needs to match the one specified in
> setup.py). E.g:
> scipion installp -p path/to/pluginName --devel
> scipion installp -p
> https://github.com/someOrg/pluginName.git --devel
> -j j Number of CPUs to use for compilation
>
> Example: scipion installp -p scipion-em-motioncorr 1.0.6 -p
> scipion-em-relion -p scipion-em-eman2
>
> Available plugins: ([ ] not installed, [X] seems already installed)
>
> scipion-em 3.0.6 [X]
> scipion-em-appion [ ]
> scipion-em-atomstructutils [ ]
> scipion-em-atsas [ ]
> scipion-em-bamfordlab [ ]
> scipion-em-bsoft [ ]
> scipion-em-ccp4 [ ]
> scipion-em-chimera [ ]
> scipion-em-cistem [ ]
> scipion-em-continuousflex [ ]
> scipion-em-cryoassess [ ]
> scipion-em-cryodrgn [ ]
> scipion-em-cryoef [ ]
> scipion-em-cryosparc2 [ ]
> scipion-em-deepfinder [ ]
> scipion-em-dynamo [ ]
> scipion-em-eman2 3.1.1 [X]
> scipion-em-empiar [ ]
> scipion-em-emxlib [ ]
> scipion-em-facilities [ ]
> scipion-em-fsc3d [ ]
> scipion-em-gautomatch [ ]
> scipion-em-gctf [ ]
> scipion-em-imagic [ ]
> scipion-em-imod [ ]
> scipion-em-localrec [ ]
> scipion-em-locscale [ ]
> scipion-em-motioncorr 1.0.6 [X]
> scipion-em-novactf [ ]
> scipion-em-phenix [ ]
> scipion-em-pyseg [ ]
> scipion-em-relion 3.0.0b7 [X]
> scipion-em-reliontomo [ ]
> scipion-em-resmap [ ]
> scipion-em-sidesplitter [ ]
> scipion-em-sphire [ ]
> scipion-em-spider [ ]
> scipion-em-tomo 3.0.6 [X]
> scipion-em-tomoj [ ]
> scipion-em-topaz [ ]
> scipion-em-xmipp 20.7.2 [X]
> scipion-em-xmipp2 [ ]
> scipion-em-xmipptomo [ ]
>
> ###########################################
>
> I am further confused as to why this would point to relion 3.0, even
> though the final lines in the Scipion plugin manager-based installation
> seemed to point to the 3.1 version.
>
> ###########################################
>
> 04565: Building scipion-em-relion ...
> 04566: /home/hilvertg/anaconda3/envs/.scipion3env/bin/python -m pip
> install scipion-em-relion==3.0.0b7
> 04567: Done (1.36 seconds)
> 04568: Building relion-3.1.0 ...
> 04569: wget -nv -c -O /home/hilvertg/software/em/relion-3.1.0.tgz.part
> https://github.com/3dem/relion/archive/3.1.0.tar.gz
> 04570: mv -v /home/hilvertg/software/em/relion-3.1.0.tgz.part
> /home/hilvertg/software/em/relion-3.1.0.tgz
> 04571: cd /home/hilvertg/software/em
> 04572: tar -xf relion-3.1.0.tgz
> 04573: cd /home/hilvertg/software/em/relion-3.1.0
> 04574: cmake -DGUI=OFF -DCMAKE_INSTALL_PREFIX=./ .
> 04575: cd /home/hilvertg/software/em/relion-3.1.0
> 04576: make -j 4
> 04577: Skipping command: Link 'relion-3.1.0 -> relion-3.1.0'
> 04578: All targets exist.
> 04579: Done (3 m 57 s)
>
> ############################################
>
> Any idea what I need to do to import my particles?
>
> Thanks,
>
> Stephan
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
