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
- Please follow installation instructions from: http://sphire.mpg.de/wiki/doku.php?id=downloads:cryolo_1&redirect=1 in order to install:
crYOLO (last tested version: 1.3.3) (should download a file called cryolo-X.Y.Z.tar.gz)
crYOLO’s boxmanager (last tested version: 1.1.0). (should download a file called cryoloBM-X.Y.Z.tar.gz) Note: the BoxManager is not strictly necessary for using the Scipion protocols.
If you want to use the generic model, please download also the General PhosaursNet model. (latest at the time of writing: ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_phosnet_20190314.h5, but better to check the Sphire page for the latest one)
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.gzScipion 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_modelInstall Scipion crYOLO Plugin
scipion installp -p scipion-em-sphireOR
through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
OR
scipion python -m pip install scipion-em-sphireIf you are developing the plugin, other useful options are:
scipion installp -p local/path/to/scipion-em-sphire --develOR
git clone git@github.com:scipion-em/scipion-em-sphire
export PYTHONPATH=$PYTHONPATH:$PWD/scipion-em-sphireRunning crYOLO tests
To check that everything is properly installed and configured, you might want to run some tests:
scipion test --grep cryolo --runRelease history Release notifications | RSS feed
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