Pre-requisites

Client pre-requisites

Apollo is a web-based application, so the only client side requirement is a web browser. Apollo has been tested on Chrome, Firefox, and Safari and matches the web browser requirements for JBrowse (see jbrowse.org for details).

Server-side pre-requisites

Note: see the Apollo 2.x quick-start for the quickest way to take care of pre-requisites.

  • System pre-requisites (see quick-start guide for simple setup)
    • Any Unix like system (e.g., Unix, Linux, Mac OS X).
    • Servlet container (must support servlet spec 3.0+) such as tomcat 8 for production (not needed for development).
    • Java 8+ OpenJDK or Oracle should work.
    • npm 2.X or better / node.js
    • Grails (optional, but good for development). The easiest way to install is using sdkman, see Apollo 2.x quick-start for this step).
    • Ant 1.8+ (most package managers will have this).
    • A database (RDMS) system. Sample configurations for PostgreSQL and MySQL are available. H2 configuration does not require any manual installation.
    • Basic tools like Git, Curl, a text editor, etc.
  • Data generation pipeline pre-requisites (for full list see http://gmod.org/wiki/JBrowse_Configuration_Guide)
    • System packages:
      • libpng12-0 (optional, for JBrowse imagetrack)
      • libpng12-dev (optional, for JBrowse imagetrack)
      • zlib1g (Debian/Ubuntu)
      • zlib1g-dev (Debian/Ubuntu)
      • zlib (RedHat/CentOS)
      • zlib-devel (RedHat/CentOS)
      • libexpat1-dev (Debian/Ubuntu)
      • expat-dev (RedHat/CentOS)
  • Perl pre-requisites:
    • Apollo will automatically try to install all perl-pre-requisites.
    • If you are building Apollo in "release" mode, perl 5.10 or up will be required
  • Sequence search (optional).
    • Blat (download Linux or OSX binaries).

Package manager commands

To install system pre-requisites, you can try the following commands

Debian/Ubuntu 16

sudo apt-get install openjdk-8-jdk curl libexpat1-dev postgresql postgresql-server-dev-all tomcat8 git

CentOS/RedHat

sudo yum install postgresql postgresql-server postgresql-devel expat-devel tomcat git curl

MacOSX/Homebrew

brew install postgresql tomcat git