Guides¶

Backup data¶

Backup your database with these commands:

docker exec Chado_DB_4_TBro_official pg_dump -U tbro -d chado | xz >tbro_backup_$(date +%F_%T).sql.xz
docker exec Worker_DB_4_TBro_official pg_dump -U worker -d worker | xz >worker_backup_$(date +%F_%T).sql.xz

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.

Replace the tbro_apache container
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¶

See the write up by 000generic at https://github.com/TBroTeam/TBro/issues/48

TBro in Docker in Amazon’s AWS Lightsail¶

Follow this protocol: https://benchling.com/s/prt-DHSo7HeddC5zM0x7x1Y4