1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
  7. SeqWare Web Service
  8. SeqWare Query Engine
  9. Glossary
  10. Frequently Asked Questions
  11. APIs
  12. Source Code
  13. Plugins
  14. Modules
  15. Advanced Topics

SeqWare Portal - Install Guide


The Portal is built and unit tested as with any other SeqWare component, using:

mvn clean install (builds and runs unit tests)



These requirements are based on what I’m using for development. You may be able to use older/newer versions but they may or may not work. You’ll find many of the required jars in the lib directory in svn.

This is what you’ll need to build/run the web applications:

  • apache-tomcat >= 6.0.13
  • Java SE >= 1.6
  • Java EE >= 5
  • postgresql >= 8.1.3
  • PostgreSQL JDBC Driver (postgresql-jdbc3.jar)
  • apache-ant >= 1.7.0
  • hibernate >= 3.2
  • spring-framework >= 2.1


If you just want to get a copy installed without compiling, perform the following steps:

  • Download and install apache-tomcat, postgresql and java. Typically this involves using yum or apt-get depending on your Linux distribution. You can also install manually. The steps below assume your apache tomcat install is located in //apache-tomcat-6.0.13/ If you installed via yum/apt-get the location of config/war files may be different and the way you start the server may be different as well.

  • Follow the SeqWare MetaDB install guide to setup your SeqWare MetaDB

  • Copy target/seqware-portal-.war to the apache-tomcat-6.0.13/webapps directory of your tomcat installation

  • In tomcat, create the subdirectory apache-tomcat-6.0.13/conf/Catalina/localhost/

  • Copy target/seqware-portal-.xml to apache-tomcat-6.0.13/conf/Catalina/localhost

  • Copy web/WEB-INF/lib/postgresql-jdbc3.jar to apache-tomcat-6.0.13/lib/

  • Modify apache-tomcat-6.0.13/conf/Catalina/localhost/seqware-portal-.xml to reflect the correct username, password and url for your database.

Starting the Web Service

  • You can now start the server using the apache-tomcat-6.0.13/bin/startup.sh script and you can stop the server using the shutdown.sh script.

  • Once the service is running you should be able to load http://localhost:8080/seqware-portal-, register an account, and start setting up SeqWare experiments.

  • There is a default admin user setup in the seqware_meta_db. The username is ‘admin@admin.com’ and the password is ‘admin’. Make sure you update this account in the seqware_meta_db before making your SeqWare Portal publicly available.