Hi,
I'm not familiar with either tomcat or centos 6 (I use centos 7 personally)...
The first issue is, you can only use certbot-auto with centos 6...
After that, please try this post
You'll need to ignore all commands with apt-get.
Don't forget to use ./certbot-auto in place of certbot (and you should run all certbot-auto commands under the correct directory)
P.S. I'm not sure if certbot-auto will run correctly on centos 5...
Do you know you could use clients other than certbot?
Check it out here: ACME Client Implementations - Let's Encrypt
Thank you