Apollo2Build.md

Web Apollo 2.0 build instructions

View On GitHub

Install Grails:

1. curl -s get.gvmtool.net | bash
2. gvm install grails 2.4.4

Get The code

• git clone https://github.com/GMOD/Apollo.git Apollo
• cd Apollo

Basic configuration

Web Apollo 2.0 simplifies and expands options for the database setup. This section will cover the basic options for this.

Database options

Configure for H2:

• copy sample-h2-apollo-config.groovy to apollo-config.groovy and update the data directory

Configure for PostgreSQL:

• Create a new database (e.g. default is just named apollo)
• Copy sample-postgres-apollo-config.groovy to apollo-config.groovy and re-run apollo deploy
• Note: There is no need to run the old add-tracks/add-users/set-track-permissions pipeline now.

Configure for MySQL:

• Create a new database (e.g. apollo by default)
• Copy sample-mysql-apollo-config.groovy to apollo-config.groovy and re-run apollo deploy

Deploy the code as a war file

• ./apollo deploy
• copy the war file at target/apollo-X.Y.war to your webapps folder as apollo.war or similar

Login to the web interface

After deployment, you can navigate to your server at http://localhost:8080/apollo/ or similar path and you will be prompted for login information

Figure 1. "Register First Admin User" screen allows you to create a new admin user.

Figure 2. Navigate to the "Organism tab" and select "Create new organism". Then enter the new information for your organism. Importantly, the data directory refers to a directory that has been prepared with the JBrowse data loading scripts from the command line. See the data loading section for details.

Figure 3. Open up the new organism from the drop down tab on the annotator panel.