Add guide to upgrade TBro

docs/guides.rst

@@ -11,6 +11,44 @@ Backup your database with these commands::
 
 You should keep a copy of you blast `.zip` files as well.
 
+Upgrade TBro
+------------
+
+If you want to upgrade TBro to a new version (running docker) you have two options.
+
+1. Replace the ``tbro_apache`` container
+2. Upgrade in the existing container
+
+.. ATTENTION::
+    Those methods will allow you to keep your databases and all of its content.
+    However, before you upgrade check for breaking changes in the Changes section of the README.
+    And always backup your data. You should do this regularly anyway but especially before performing an upgrade.
+
+Choose option 1 if you did not modify anything inside the ``tbro_apache`` container.
+Just execute the following commands::
+
+    docker stop TBro_official
+    docker rm TBro_official
+    docker pull tbroteam/tbro_apache
+    docker run -d --link Chado_DB_4_TBro_official:CHADO --link Worker_FTP_4_TBro_official:WORKERFTP --link Worker_DB_4_TBro_official:WORKER --name "TBro_official" -p 80:80 tbroteam/tbro_apache
+    docker exec -i -t TBro_official /home/tbro/build_installation.sh
+
+For option 2 follow these steps::
+
+    docker exec -it TBro_official /bin/bash
+    # inside the container
+    source ~/.bash_profile
+    cd /home
+    git clone https://github.com/TBroTeam/TBro.git
+    # you now have tbro (old) and TBro (new) in /home
+    cd TBro
+    # git checkout <branch> # if you want a specific branch instead of master
+    cp ../tbro/build.properties .
+    phing cli-install
+    phing web-install
+    phing database-update-modifications
+
+
 Password protect TBro
 ---------------------