Thanks to the help provided, this is what I came up with.
Create a script that checks if your partition is mounted, if not mount it. After the check execute calibre. %f is so that it opens only one window(more)
#!/bin/bash
if ! grep -q /dev/sda2 /proc/mounts; then
udisksctl mount --block-device /dev/sda2
fi
calibre %f
Copy calibre from /usr/share/applications
put it on desktop. Edit it and add the script so that it is executed when you double click instead of just opening the program:
Exec=sh /home/<usr_name>/path/to/script/mount.sh
It should look something like this:
#!/usr/bin/env xdg-open
[Desktop Entry]
Type=Application
Name=calibre
GenericName=E-book library management
GenericName[de]=E-Book Bibliotheksverwaltung
Comment=E-book library management
Comment[es]=aplicación para la gestión de libros electrónicos
Comment[de]=E-Book Bibliotheksverwaltung
Exec=sh /home/<usr_name>/path/to/script/mount.sh
Icon=calibre-gui
Categories=Office;Database;FileTools;Viewer;Qt;
MimeType=x-content/ebook-reader;