Setup guide¶

The quick-start guide showed how to quickly launch a temporary instance of Apollo, but deploying the application to production normally involves some extra steps.

The general idea behind your deployment is to create a apollo-config.groovy file from some existing sample files which have sample settings for various database engines.

Production pre-requisites¶

You will minimally need to have Java 8 or greater, Grails, git, ant, a servlet container e.g. tomcat7+, jetty, or resin. An external database such as PostgreSQL or MySQL is generally used for production, but instructions for the H2 database is also provided.

Important note: The default memory for Tomcat and Jetty is insufficient to run Apollo (and most other web apps).You should increase the memory according to these instructions.

Other possible build settings for JBrowse (based on an Ubuntu 16 install):

 sudo apt-get update && sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential git python-software-properties 
 curl -sL https://deb.nodesource.com/setup_6.x | sudo -E bash -
 sudo apt-get install nodejs 

NOTE: npm (installed with nodejs) must be version 6 or better. If not installed from the above instructions, most stable versions of node.js will supply this. nvm may also be useful.

NOTE: you must link nodejs to to node if your system installs it as a nodejs binary instead of a node one. E.g.,

sudo ln -s /usr/bin/nodejs /usr/bin/node

Build settings for Apollo specifically. Recent versions of tomcat7 will work, though tomcat8 is preferred. If it does not install automatically there are a number of ways to build tomcat on linux:

sudo apt-get install ant openjdk-8-jdk 
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/  # or set in .bashrc / .project

Download Apollo from the latest release under source-code and unzip. Test installation by running ./apollo run-local and see that the web-server starts up on http://localhost:8080/apollo/. To setup for production continue onto configuration below after install .

If you get an Unsupported major.minor error or similar, please confirm that the version of java that tomcat is running ps -ef | grep java is the same as the one you used to build. Setting JAVA_HOME to the Java 8 JDK should fix most problems.

JSON in the URL with newer versions of Tomcat¶

When JSON is added to the URL string (e.g., addStores and addTracks) you may get this error with newer patched versions of Tomcat 7.0.73, 8.0.39, 8.5.7:

 java.lang.IllegalArgumentException: Invalid character found in the request target. The valid characters are defined in RFC 7230 and RFC 3986

To fix these, the best solution we’ve come up with (and there may be many) is to explicitly allow these characters, which you can do starting with Tomcat versions: 7.0.76, 8.0.42, 8.5.12. This is done by adding the following line to $CATALINA_HOME/conf/catalina.properties:

tomcat.util.http.parser.HttpParser.requestTargetAllow=|{}

Database configuration¶

Apollo supports several database backends, and you can choose sample configurations from using H2, Postgres, or MySQL by default.

Each has a file called sample-h2-apollo-config.groovy or sample-postgres-apollo-config.groovy that is designed to be renamed to apollo-config.groovy before running apollo deploy. Additionally there is a sample-docker-apollo-config.groovy which allows control of the configuration via environment variables.

Furthermore, the apollo-config.groovy has different groovy environments for test, development, and production modes. The environment will be selected automatically selected depending on how it is run, e.g:

apollo deploy or apollo release use the production environment (i.e. when you copy the war file to your production server apollo run-local or apollo debug use the development environment (i.e. when you are running it locally)
apollo test uses the test environment (i.e. only when running unit tests)

Configure for H2:¶

H2 is an embedded database engine, so no external setups are needed. Simply copy sample-h2-apollo-config.groovy to apollo-config.groovy.
- The default dev environment (apollo run-local or apollo run-app) is in memory so you will have to change that to file.
If you use H2 with tomcat or jetty in production you have to set the permissions for the file path in production correctly (e.g. jdbc:h2:/mypath/prodDb, chown -u tomcat:tomcat /mypath/prodDb.*.db).
- If you use the local relative path jdbc:h2:./prodDb and tomcat8 the path will likely be: /usr/share/tomcat8/prodDb*db

Configure for PostgreSQL:¶

Create a new database with postgres and add a user for production mode. Here are a few ways to do this in PostgreSQL.
Copy the sample-postgres-apollo-config.groovy to apollo-config.groovy.

Configure for MySQL:¶

Create a new MySQL database for production mode (i.e. run ``create database `apollo-production``` in the mysql console) and copy the sample-postgres-apollo-config.groovy to apollo-config.groovy.

Configure for Docker:¶

Set up and export all of the environment variables you wish to configure. At bare minimum you will likely wish to set WEBAPOLLO_DB_USERNAME, WEBAPOLLO_DB_PASSWORD, WEBAPOLLO_DB_DRIVER, WEBAPOLLO_DB_DIALECT, and WEBAPOLLO_DB_URI
Create a new database in your chosen database backend and copy the sample-docker-apollo-config.groovy to apollo-config.groovy.
Instructions and a script for launching docker with apollo and PostgreSQL.

Apollo in Galaxy¶

Apollo can always be used externally from Galaxy, but there are a few integrations available as well.

Database schema¶

After you startup the application, the database schema (tables, etc.) is automatically setup. You don’t have to initialize any database schemas yourself.

Deploy the application¶

The apollo run-local command only launches a temporary server and should really not be used in production, so to deploy to production, we build a new WAR file with the apollo deploy command. After you have setup your apollo-config.groovy file, and it has the appropriate username, password, and JDBC URL in it, then we can run the command:

./apollo deploy

This command will package the application and it will download any missing pre-requisites (jbrowse) into a WAR file in the “target/” subfolder. After it completes, you can then copy the WAR file (e.g. apollo-2.0.4.war) from the target folder to the web-app folder of your web container installation. If you name the file apollo.war in your webapps folder, then you can access your app at “http://localhost:8080/apollo”

We test primarily on Apache Tomcat (7.0.62+ and 8). Make sure to set your Tomcat memory to an appropriate size or Apollo will run slow / crash.

Alternatively, as we alluded to previously, you can also launch a temporary instance of the server which is useful for testing

./apollo run-local 8085

This temporary server will be accessible at “http://localhost:8085/apollo”

Tomcat configuration¶

If you have tracks that have deep nested features that will result in a feature JSON larger than 10MB or if you have a client that sends requests to the Apollo server as JSON of size larger than 10MB then you will have to modify src/war/templates/web.xml.

Specifically the following block in web.xml:

    <context-param>
        <param-name>org.apache.tomcat.websocket.textBufferSize</param-name>
        <param-value>10000000</param-value>
    </context-param>
    <context-param>
        <param-name>org.apache.tomcat.websocket.binaryBufferSize</param-name>
        <param-value>10000000</param-value>
    </context-param>

Note: The <param-value> is in bytes.

Memory configuration¶

Changing the memory used by Apollo in production must be configured within Tomcat directly.

The default memory assigned to Apollo to run commands in Apollo is 2048 MB. This can be changed in your apollo-config.groovy by uncommenting the memory configuration block:

// Uncomment to change the default memory configurations
grails.project.fork = [
        test   : false,
        // configure settings for the run-app JVM
        run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
        // configure settings for the run-war JVM
        war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
        // configure settings for the Console UI JVM
        console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
]

Note on database settings¶

If you use the apollo run-local command, then the “development” section of the apollo-config.groovy is used (or an temporary in-memory H2 database is used if no apollo-config.groovy exists).

If you use the WAR file generated by the apollo deploy command on your own webserver, then the “production” section of the apollo-config.groovy is used.

Detailed build instructions¶

While the shortcut apollo deploy takes care of basic application deployment, understanding the full build process of Apollo can help you to optimize and improve your deployed instances.

To learn more about the architecture of webapollo, view the architecture guide but the main idea here is to learn how to use apollo release to construct a build that includes javascript minimization

Pre-requisites for Javascript minimization¶

In addition to the system pre-requisites, the javascript compilation will use nodejs, which can be installed from a package manager on many platforms. Recommended setup for different platforms:

sudo apt-get install nodejs
sudo yum install epel-release npm
brew install node

Install extra perl modules¶

Building apollo in release mode also requires some extra Perl modules, namely Text::Markdown and DateTime. One way to install them:

bin/cpanm -l extlib DateTime Text::Markdown

Performing the javascript minimization¶

To build a Apollo release with Javascript minimization, you can use the command

./apollo release

This will compile JBrowse and Apollo javascript code into minimized files so that the number of HTTP requests that the client needs to make are reduced.

In all other respects, apollo release is exactly the same as apollo deploy though.

Performing active development¶

To perform active development of the codebase, use

./apollo debug

This will launch a temporary instance of Apollo by running grails run-app and ant devmode at the same time, which means that any changes to the Java files will be picked up, allowing fast iteration.

If you modify the javascript files (i.e. the client directory), you can run scripts/copy_client.sh and these will be picked up on-the-fly too.