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Sphire ready to use in scipion.

Project description

Plugin to use Sphire programs within the Scipion framework

So far we have implemented:

  • crYOLO particle picker (current version: 1.3.3)

crYOLO installation

The installation should be pretty easy if you have already a conda installation.

conda create -n cryolo -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5
pip install cryolo-X.Y.Z.tar.gz
pip install cryoloBM-X.Y.Z.tar.gz

Scipion crYOLO Configuration

Then, we need to define some environment variables to specify how to load the cryolo environment and where is the general model. We can define the variables in the .bashrc file or in ~/.config/scipion/scipion.conf:

CRYOLO_ENV_ACTIVATION = '. /path/to/anaconda/etc/profile.d/conda.sh; conda activate cryolo'
CRYOLO_GENERIC_MODEL = path/to/the/downloaded/General_PhosaursNet_model

Install Scipion crYOLO Plugin

scipion installp -p scipion-em-sphire

OR

  • through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

OR

scipion python -m pip install scipion-em-sphire

If you are developing the plugin, other useful options are:

scipion installp -p local/path/to/scipion-em-sphire --devel

OR

git clone git@github.com:scipion-em/scipion-em-sphire
export PYTHONPATH=$PYTHONPATH:$PWD/scipion-em-sphire

Running crYOLO tests

To check that everything is properly installed and configured, you might want to run some tests:

scipion test --grep cryolo --run

Project details


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Files for scipion-em-sphire, version 1.2.7
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