Menu entries

As we want to propose several versions of the tools, each piece of software should have its own submenu under VNM Neuroimaging. To do so, you first have to add a submenu to menus/vnm-applications.menu by adding:

<!-- [[Tool Name]] submenu -->
<Menu>
    <Name>[[Tool Name]]</Name>
    <Directory>vnm-[[tool-name]].directory</Directory>
    <Include>
        <And>
            <Category>[[Tool-Name]]</Category>
        </And>
    </Include>
</Menu> <!-- End [[Tool Name]] -->

The following table shows the formatting rules to follow:

Next, we have to create the submenu itself as we referenced it by vnm-[[tool-name]].directory. To do so, create the file menus/submenus/vnm-[[tool-name]].directory and add the following information inside:

[Desktop Entry]
Name=[[Tool Name]]
Comment=[[Tool Name]]
Icon=/home/neuro/.config/lxpanel/LXDE/icons/[[icon-name]].png
Type=Directory

If a specific icon is available in the menus/icons directory, replace [[icon-name]] by its name. Otherwise, use vnm.

Create the application

Finally, we have to create the actual application by creating the file menus/applications/vnm-[[tool-name]]-[[0.0.0]].desktop. The name of this file must contain the version of the tool (once again to allow multiple versions to live inside the same directory). Add the following description to this file:

[Desktop Entry]
Name=[[Tool Name]] [[0.0.0]] [[(Install only)]]
GenericName=[[Tool Name]] [[0.0.0]]
Comment=The description of what clicking on this application does. # This will be the tooltip of the application.
Exec=The command used to run the application.
Icon=/home/neuro/.config/lxpanel/LXDE/icons/[[icon-name]].png
Type=Application
Categories=[[Tool-name]]
Terminal=true # or false

The important part here is the value of Exec. If the tool is in the form of a singularity image, you should run the following command:

bash /usr/share/fetch_and_run.sh [[tool-name]] [[0.0.0]] [[YYYYMMDD]] [[cmd]] [[args]]

What fetch_and_run.sh does is check if the image is already installed as a module. If not, it checks whether it can be installed or not (return 1 if not possible). After that, it installs the image as a module. If [[cmd]] is specified, once the image is installed, it runs the command by giving the arguments from [[args]]. Here are two examples for FreeSurfer and FreeView. This first one only installs the image as a module:

bash /usr/share/fetch_and_run.sh freesurfer 6.0.1 20200506

And this does the same but runs FreeView afterward:

bash /usr/share/fetch_and_run.sh freesurfer 6.0.1 20200506 freeview

The resulting .desktop file corresponding to FreeView contains:

[Desktop Entry]
Name=FreeView 6.0.1
GenericName=FreeView 6.0.1
Comment=Start FreeView 6.0.1
Exec=bash /usr/share/fetch_and_run.sh freesurfer 6.0.1 20200506 freeview
Icon=/home/neuro/.config/lxpanel/LXDE/icons/run.png
Type=Application
Categories=FreeSurfer
Terminal=true