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Last pushed: 2 years ago
Short Description
FlyBase implementation of InterMine.
Full Description

FlyBase InterMine (FlyBaseMine)

Dockerized FlyBase implementation of the InterMine software.

Getting Started With FlyBaseMine

Initial setup

Pull and run the FlyBase InterMine Database image, changing the username and password
to values of your choosing.

docker run --name intermine-db -e POSTGRES_USER=intermine -e POSTGRES_PASSWORD=intermine -d flybase/intermine-db

Pull and run the FlyBase Tomcat image, be sure to change the user and password values for the manager user.

docker run --name intermine-tomcat -d --link intermine-db:db -p 8080:8080 -e TOMCAT_MANAGER_USER=intermine -e TOMCAT_MANAGER_PASSWORD=intermine flybase/intermine-tomcat

The --link flag tells docker to link the intermine-db container from the first line above to the tomcat conatiner and
make the alias db on the tomcat instance. In other words, db is how you will reference the database hostname
on the tomcat instance. If you change the db alias you will need to update $HOME/.intermine/
on the build container.

If your host machine already has something binding port 8080, change the -p to <newport>:8080.


docker run --name intermine-tomcat -d --link intermine-db:db -p 8888:8080 -e TOMCAT_MANAGER_USER=intermine -e TOMCAT_MANAGER_PASSWORD=intermine flybase/intermine-tomcat

Pull and run the FlyBase InterMine build image.

docker run -it -v /localhost/path/to/flybasemine_data:/data --name intermine-build --link intermine-db:db --link intermine-tomcat:tomcat flybase/intermine bash

The -v flag maps the host machine directory /localhost/path/to/flybasemine_data to the /data directory in the container.
If you omit the -v flag it will create an empty data directory on your container that you will have to populate with data files. See
the /intermine/flybasemine/project.xml file for their expected names and locations.

Starting / Stopping

Once you have done the intial setup, you can start and stop the containers with the
docker start <container_name>
docker stop <container_name>

Note: Container links are specific to each container. If you remove the database container you will need to create new tomcat and build containers as detailed in Initial Setup relink them.


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