From Cheaha
Revision as of 22:38, 7 January 2012 by (talk | contribs)
Jump to navigation Jump to search

Attention: Research Computing Documentation has Moved

Please use the new documentation url for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team


CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service.

Web Resources (Links)

Installation notes for Intermine on Ubuntu 64bit

Step A: Install all prerequistite tools required for Intermine installation

The basic notes for Installation are present on the Intermine website at

Additional install notes . This Installation is done on a Virtual box (running on win 7 64bits).

1. Install subversion

  sudo apt-get install subversion

2. Install sunjava6jdk

  sudo add-apt-repository "deb lucid partner" (added a source repository)
  Or add following to the /etc/apt/osurcelist
  deb lucid partner
  deb-src lucid partner
  Commands to run - 	
  sudo apt-get update
  sudo apt-get install sun-java6-jdk

3. Install ant

  a. Download ant from or
  b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-
  c. export ANT_HOME=/home/ranjit/ant    (ant is in my home directory)
  d. export PATH=${PATH}:${ANT_HOME}/bin
  These variable can be included in a batch script which automatically runs after system login. 

4. Install Tomcat

  Download tomcat, unzip it and place it at a location you know.
  Just start/stop the server as (ant is in my home directory)
  /home/ranjit/apache-tomcat-6.0.33/bin/ (to start the server)
  /home/ranjit/apache-tomcat-6.0.33/bin/  (to stop it)		
  Add a manager for tomcat by editing file  $CATALINA_HOME/conf/tomcat-users.xml   ($CATALINA_HOME is the installation directory)
  <role rolename="manager"/>
  <user username="manager" password="manager" roles="manager"/>
  Add java memmory requirements
  To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/ You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR
  Edit the file $TOMCAT_HOME/bin/ and insert the following line, substituting for the desired value, eg. Bash Shell:  export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”
  If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.

5. Install postgresql 8.4

  sudo apt-get install postgresql-8.4
  Make following changes in file as suggested in postgre installation section of intermine page at
  sudo vim /etc/postgresql/8.4/main/postgresql.conf
  Create/Identify a userid and password. (help
  Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf   to use "md5" MD5 authentication
  sudo /etc/init.d/postgresql-8.4 restart         (restart the server)
  Install Bioseg into postgres
  sudo apt-get install postgresql-contrib-8.4
  sudo apt-get install postgresql-server-dev-8.4
  Download bioseg from   
  Unzip and Install it as
  make USE_PGXS=t clean
  make USE_PGXS=t
  make USE_PGXS=t install
  When a database is created it can be added to it by
  psql (database) <bioseg.sql
  psql (database) <btree_gist.sql
  To start/stop/restart postgressql do..
  sudo /etc/init.d/postgresql-8.4 start    (replace start with stop/restart)

6.Install Junit

  Download from
  Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)
  Add to the java classpath with this command, replacing X.X with the version number.
  export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar