breedbase_dockerfile

The Dockerfiles for breeDBase

Install docker (on Debian/Ubuntu)

apt-get install docker-ce

Clone the repo

git clone https://github.com/solgenomics/breedbase_dockerfile

Run the prepare.sh script from within the breedbase_dockerfile dir

cd breedbase_dockerfile
./prepare.sh

This will clone all the git repos that are needed for the build into a directory called repos/. You can then checkout particular branches or tags in the repo before the build.

Build the image

docker build -t breedbase_image breedbase_dockerfile

Create the docker config

You need to write an sgn_local.conf file specific to your service. A template is provided in the breedbase_dockerfile repo (you have to fill in the db server host, dbname, and username and password). Then:

cat sgn_local.conf | docker config create "breedbase_sgn_local.conf" -

Run the service using swarm

To run the docker on the swarm, you have to provide the config using --config, as well as any mounts that are required for presistent data. Currently, breedbase just mounts directories on the docker host (which can be nfs mounts), but later this could be changed to docker volumes. Multiple mountpoints can be provided with multiple --mount options, as follows:

docker service create --name "breedbase_service" --mount src=/export/prod/archive,target=/home/production/archive,type=bind --mount src=/export/prod/public_breedbase,target=/home/production/public,type=bind --config source="breedbase_sgn_local.conf",target="/home/production/cxgn/sgn/sgn_local.conf"  breedbase_image

Debugging

The service should be visible on that host now. To debug, log into the container. You can find the container id using

docker ps

then

docker exec -it <container_id> bash

You can use lynx localhost:8080 to see if the server is running correclty within the docker, and look at the error log usign tail -f /var/log/sgn/error.log or less /var/log/sgn/error.log.

You can of course also find the IP address of the running container either in the container using ip address or from the host using docker inspect <container_id>.

Set up forwarding in host using nginx

Finally, set up nginx or apache2 forwarding to the container. It is recommended to use a secure http connection (https).

Docker Hub

You should be able to download the latest images from docker hub, at hub.docker.com, breedbase/breedbase:latest, using

docker pull breedbase/breedbase:latest