GMOD/docker-apollo

Name: docker-apollo

Owner: Generic Model Organism Database Project

Description: :whale: Apollo 2.X Docker Image

Forked from: hdzierz/docker-webapollo2

Created: 2016-05-04 15:47:57.0

Updated: 2017-07-08 04:07:50.0

Pushed: 2017-12-20 23:37:51.0

Homepage:

Size: 278

Language: Groovy

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

Apollo

Apollo is a browser-based tool for visualisation and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process.

Running the Container

The container is publicly available as gmod/apollo:latest.

There are a large number of environment variables that can be adjusted to suit your site's needs. These can be seen in the apollo-config.groovy file.

Quickstart

This procedure starts tomcat in a standard virtualized environment with a PostgreSQL database with Chado.

Install docker for your system if not previously done.

Choose an option:

• To test a versioned release to test installation, e.g.: docker run -it -p 8888:8080 quay.io/gmod/docker-apollo:2.0.8 Other available versions

• Install a latest release to test installation: docker run -it -p 8888:8080 gmod/apollo:latest

• To make sure you have the latest pull with `docker pull gmod/apollo` to fetch newer versions

• If using within a larger context (e.g., as part of a docker-compose script) you can run an `apollo-only` branch provides only apollo + tomcat (no PostgreSQL):
  

• docker run -it -p 8888:8080 gmod/apollo:apollo-only

• To run in production against JBrowse data and a persistent database (you can create an empty directory called postgres-data):
  

  • docker run -it -v /jbrowse/root/directory/:/data -v postgres-data:/var/lib/postgresql -p 8888:8080 gmod/apollo:latest

• You can run production using the build created by quay.io instead (https://quay.io/repository/gmod/docker-apollo):

  • docker run -it -v /jbrowse/root/directory/:/data -v postgres-data:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:latest

In all cases, Apollo will be available at http://localhost:8888/ (or 8888 if you don't configure the port)

When you use the above mount directory `/jbrowse/root/directory` and your genome is in

: If you don't use a locally mounted PostgreSQL database (e.g., creating an empty directory and mounting using `-v postgres-data:/var/lib/postgresql`)
set appropriate environment variables](https://docs.docker.com/engine/reference/commandline/run/) for a remote database 
e variables [defined here](https://github.com/GMOD/docker-apollo/blob/master/launch.sh)) your annotations and setup will not be persisted.

Logging In

default credentials in this image are:

edentials |                    |
-         | ------------------ |
ername    | `admin@local.host` |
ssword    | `password`         |


Example Workflow


ake the following directories somewhere with write permissions: `postgres-data` and `jbrowse-data`. 
opy your jbrowse data into `jbrowse-data`.  We provide [working sample data](http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#adding-sample-data).
un the docker-command:  `docker run -it -v /absolute/path/to/jbrowse-data:/data -v /absolute/path/to/postgres-data:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:latest`
ogin to the server at `http://localhost:8888/`
dd an organism per the [instructions under Figure 2](http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#login-to-the-web-interface).   Using yeast as an example, if you copy the data into `jbrowse-data/yeast` then on the server 
ll add the directory: `/data/yeast`. 

./img/small-sample.png)

Chado

o support is now baked into the GMOD docker container image.