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Re: [scipion-users] warnings about missing plugins and CONDA
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From: Daniel L. <dan...@ic...> - 2019-11-01 10:14:19
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On 2019-10-31, at 11:32, Pablo Conesa <pc...@CN...<mailto:pc...@CN...>> wrote:
Hi Daniel,
About XMIPP:
You probably have the plugin (python code that wrapps xmipp) but not the actual xmipp.
Try scipion installb
I'm getting:
xmippBin_Centos 3.19.04 [ ]
xmippBin_Debian 3.19.04 [ ]
xmippSrc 3.19.04 [X]
First ones are compiled xmipp for Centos and Debian.
3rd are sources and will require compiling xmipp, but probably safer in terms of dependencies.
Running "scipion installb" revealed that I indeed do not have xmipp installed. I did not realize that you could drill down for Xmipp in the Plugin Manager GUI. When I tried installing xmippSrc, it turns out that I have a too old g++ compiler (needs 4.8 or later). I guess that is why I did not get xmipp in the first place. Now I figured out how to use g++ version 7.3.1, but run into problems with missing opencv headers. I don't think I will need such features and wondering how I should customize my installation to run with "--no-opencv". Where should I edit?
About CONDA_ACTIVATION_CMD:
Some plugins, (in your case sphire) require to have conda installed. Conda installation ask you to "add itself" to the shell so you have conda in the PATH.
When doing so, python calls, in some cases are messed up due to having conda and its python exposed in the terminal.
We recommend not to have conda initialized in the terminal and tell scipion how to activate conda using the variable "CONDA_ACTIVATION_CMD"
In my case I got this in the <Scipion-home>/config/scipion.conf under BUILD section:
CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
NOTE: Conda usually tells you that command. see https://github.com/scipion-em/scipion-em-sphire#cryolo-integration
Ok. I don't think there is Conda available. I'll uninstall Sphire/cryolo for the time being.
About Locascale: Locscale plugin has a dependency to Eman plugin, try to install eman plugin:
scipion installp -p scipion-em-eman2
Ok. Fixed that!
On 31/10/19 10:55, Daniel Larsson wrote:
So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions?
Regards,
Daniel
scipion installp --help --checkUpdates
Scipion v2.0 (2019-04-23) Diocletian
python /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates
>>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp in Scipion manager window)
> error when importing from eman2: No module named PyQt4
Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34
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.
Warning: couldn't find Plugin for scipion-em-locscale
Dirname: locscale
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
usage: /home/larsson/software/scipion_v2.0/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: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2
Available plugins: ([ ] not installed, [X] seems already installed)
scipion-em-appion 1.0.2 [X]
scipion-em-atomstructutils 1.0.7 [X]
scipion-em-atsas 1.0.6 [X]
scipion-em-bamfordlab [ ]
scipion-em-bsoft 1.0.3 [X]
scipion-em-ccp4 1.0.12 [X]
scipion-em-chimera 1.0.2 [X]
scipion-em-cryoef 1.0.5 [X]
scipion-em-cryomethods [ ]
scipion-em-cryosparc2 1.0.7 [X]
scipion-em-eman2 [ ]
scipion-em-empiar 1.0.3 [X]
scipion-em-emxlib [ ]
scipion-em-esrf [ ]
scipion-em-gautomatch 1.0.7 [X]
scipion-em-gctf 1.0.7 [X]
scipion-em-grigoriefflab 1.0.6 [X]
scipion-em-imagic [ ]
scipion-em-ispyb [ ]
scipion-em-localrec 2.0 [X]
scipion-em-locscale 1.0.5 [X]
scipion-em-motioncorr 1.0.4 [X]
scipion-em-nysbc [ ]
scipion-em-phenix [ ]
scipion-em-powerfit [ ]
scipion-em-relion 1.0.7 [X]
scipion-em-resmap 1.0.5 [X]
scipion-em-simple [ ]
scipion-em-sphire 1.2.9 [X]
scipion-em-spider [ ]
scipion-em-topaz [ ]
scipion-em-xmipp 19.4.3 [X]
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Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team
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