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This page aims to introduce you to the usage of Scipion Plugin Manager which is a friendly application to manage everything related to the installation of the Scipion plugins.
Where is it?
After launching Scipion from the command line (
./scipion ) we will see the project manager window. Here we click on the Configuration menu to select the Plugins option (Figure 1).
Figure 1. Scipion project manager
Now you will see the Plugin Manager interface (Figure 2).
Figure 2. Plugin manager
On the left we can see the list of all available plugins. Top right panel displays information for the selected plugin loaded from Pypi, such as name, version, release date, plugin description, url and the authors.
At the begining, all plugins are uninstalled and appear with the UNINSTALLED icon (). If you want to install any plugin, you need to do the following two steps.
Step 1: Check the selected plugin
We have two options:
Click on the UNINSTALLED icon .
Right-click on the plugin name and select the INSTALL option
In both cases, the selected plugin icon change to TO INSTALL icon () and the operation is shown in the bottom right panel on the Operations tab. We can select more than one plugin to install (Figure 3)
Figure 3. Installing plugins
Step 2: Execute all selected operations
Once all the operations have been selected, we will proceed to execute them. For this, on the bottom right panel we have a tool bar with the action . This action executes automatically all operations that we have selected. When you click on the icon, the Plugin manager is locked until all operations have been executed. Once all the operations have been executed, the status of the selected plugins changes as shown in the Figure 4. The selected plugins will appear as installed .
If there is an error in the installation process, the operation will appear as not executed , otherwise it will appear as executed .
Before execute all operations, we can cancel any operation by selecting it and clicking on the action or with a right-click on the plugin name and selecting Undo . In the same way, we can change the number of processors with which we want all the selected operations to be executed. By default it is 4 processors.
Figure 4. Installed plugin
Until the Plugin manager executes everything, we can check the logs on the Output log tab from the bottom right panel. The operations logs will show up in the Plugin.log tab as the Figure 5 shows. If there are errors, Plugin.error will show a detailed list of these.
Figure 5. Plugin manager logs
When a plugin is installed, the list of binaries is added to the plugin on the tree in the left panel. If we want to show the list of binaries we need to expand the plugin as shown in Figure 6. It is important to mention that only the binaries that were defined by default in the plugin will be installed. If we need to install other non-default binaries of any plugin, we just need to do the same procedure we did to install a plugin.
Figure 6. Scipion-em-grigoriefflab binaries
In the same way that we install a set of plugins, we can uninstall them. For this, we need to select an installed plugin and follow these steps.
Step 1: Uncheck the selected plugin
Again, we have two options:
- Click on the INSTALLED icon .
- Right-click on the plugin name and select the UNINSTALL option
In both cases, the selected plugin icon will change to TO UNINSTALL icon () and the operation is shown in the bottom right panel on the Operations tab. We can select more than one plugin to uninstall (Figure 7)
Figure 7. Uninstalling plugins
Step 2: Execute all selected operations
Same as Step 2 to Install Plugins
The Plugin Manager can detect when there are plugin updates available. In this case, the name of the plugin is highlighted in bold and, in the top right panel there will be information about the new version and how to update the plugin (see Figure 8).
Figure 8. Updating plugins
To update any plugin, we need to select an installed plugin, right-click on the plugin name and select the UPDATE option
In this case, the selected plugin icon will change to TO UPDATE icon and the operation is shown in the bottom right panel on the Operations tab (Figure 9)
Figure 9. Uninstalling plugins
To execute the selected operation we just need to press the execute operation icon like Install or Uninstall any plugin or binary
Plugin Manager Glosary
The Plugin Manager has a glossary of terms in the Help menu in the toolbar. This interface shows the icons that are used and their meaning as shown in the following figure.
Figure 10. Glossary