I figured it wasn’t the best solution, although I was puzzled. This is the first contained I ever had problems with. No idea why it showed that I didn’t have permission, since the user I used has permission on those directories.
But then I then had a look at the permission of the Library shared location:
You can see that it has permission to read/write because I’m in the admin group, but not because my user had read/write directly assigned to it. So I gave the user direct read/write permissions.
This change will not take effect until the container is restarted. Once restarted, doing an ls -la would show the right permissions.
myuser@synology:~$ sudo docker exec -it calibre-web ls -la /books | grep metadata
-rwx------ 1 abc users 1558528 Aug 28 18:33 metadata.db
-rwx------ 1 abc users 18422 Aug 28 18:34 metadata_db_prefs_backup.json
Before I restarted the contained, I changed the PGID back to 100, now that my user has the right permissions – and it worked!