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Sphire ready to use in scipion.

Project description

# scipion-em-sphire
Plugin to use Sphire programs within the Scipion framework

So far we have implemented:

* crYOLO Version 1.2.2

Installation
============

1. Please follow installation instructions at <http://sphire.mpg.de/wiki/doku.php?id=downloads:cryolo_1&redirect=1>

2. Install `crYOLO Version 1.2.2 <http://sphire.mpg.de/wiki/doku.php?id=cryolo_archive#cryolo>

3. Install `crYOLO boxmanager 1.1.0 <http://sphire.mpg.de/wiki/doku.php?id=cryolo_archive#cryolo>

4. If you want to use the generic model, please download the General PhosaursNet model and it the add the path in
~/.config/scipion/scipion.conf
CRYOLO_GEN_MODEL = path/to/the/downloaded/General_PhosaursNet_model

5. git clone the plugin repository to any local folder <https://github.com/scipion-em/>
git clone git@github.com:scipion-em/scipion-em-myplugin.git /home/me/myplugin

6. Install scipion-em-sphire
a) In user mode: or through the GUI menu bar
``scipion installp -p scipion-em-sphire``

OR

b, through the GUI menu bar. Please select Configuration/Plugins

7. Add the path to ~/.config/scipion/scipion.conf
CRYOLO_HOME = ~/anaconda3/envs/cryolo

Project details


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