When you do sudo mysql -u root -p the mysqld need to be running. There are some errors but a the end it is write :
[Note] mysqld: ready for connections.
You can tr to check if your conf are different of official conf with:
yunohost service regen-conf
I don’t know exactly how to help you about this corrupted mysql database. May be you can try this ?
https://wiki.labriqueinter.net/doku.php/howto:fix_self_corrupt_mysql
When you do sudo mysql -u root -p the mysqld need to be running. There are some errors but a the end it is write :
[Note] mysqld: ready for connections.
I only have this message:
ERROR 2002 (HY000): Can’t connect to local MySQL server through socket ‘/var/run/mysqld/mysqld.sock’ (2)
No feedback from this command 
I will take a look, thanks a lot for your time and help ! 
Great news !
It worked !
Oh in fact this kind of command where not working:
in another one, get the list of tables to fix
myisamchk -a *.MYI | grep error
But I just did this one:
dpkg-reconfigure mysql-server-5.5
And everything is fine now
I just have owncloud that is still not working 
But well, I have a backup of the files, so I could just reinstall it.
Well everything is working, but it seems to still use --skip-grant-tables option, and it do not allow to install a new app using the database.
Or in fact I can install it, but it raise this warning message saying that this option prevent it from creating a database.
And after a while, the issue rehappear, I need to restart mysql (using this option).
I confirm, every X hours (seems like it’s done when I stop using it) I need to kill mysql process (still running) and restart it.
I don’t understand why it stops working.
I could correct it by using a cron task to relaunch it from time to time, but I’m sure there is a smarter solution. Any idea ? 
May be you should
?
Or you can read logs to understand why at this hour it fails.
So in fact it stops when I close my terminal - even if the process is still there.
I separated it using tmux, no error.
I think it’s better to clean it indeed.
Do you know how to do that ? (tutorial ?)
Thanks