NOTICE: This repo has been integrated directly into https://github.com/GMOD/Apollo. It can be found on http://hub.docker.com/gmod/apollo or http://quay.io/repository/gmod/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.
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.
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 -v /directory/to/jbrowse/files:/data quay.io/gmod/docker-apollo:2.3.1
Other available versions
Install a latest release to test installation: docker run -it -p 8888:8080 -v /directory/to/jbrowse/files:/data gmod/apollo:latest
docker pull gmod/apollo
to fetch newer versionsTo run in production against persistent JBrowse data and a persistent database you should:
postgres-data
./jbrowse/root/directory/
.docker run -it -v /jbrowse/root/directory/:/data -v /postgres/data/directory:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:latest
See docker run instructions to run as a daemon (-d
) and with a fresh container each time (--rm
) depending on your use-case.
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
You can configure options if need be (though default will work) by setting environmental variables for apollo-config.groovy by passing through via multiple -e
parameters :
- `docker run -it -e APOLLO_ADMIN_PASSWORD=superdupersecrect -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
/jbrowse/root/directory/myawesomegenome
you'll point to the directory: /data/myawesomegenome
.
-e APOLLO_PATH=otherpath
when running.NOTE: 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
)
or set appropriate environment variables for a remote database
( see variables defined here) your annotations and setup will not be persisted.
The default credentials in this image are:
Credentials | |
---|---|
Username | admin@local.host |
Password | password |
postgres-data
and jbrowse-data
. jbrowse-data
. We provide working sample data.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
http://localhost:8888/
jbrowse-data/yeast
then on the server
you'll add the directory: /data/yeast
. Apollo run-time options are specified in the createenv.sh file.
These are picked up in the apollo-config.groovy file and follows the rules of regular apollo configuration.
Special cases include CHADO. By default it is on, but use WEBAPOLLO_USE_CHADO=false
to turn off.