Intermine

Motivation

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 for Intermine

• Home page http://www.intermine.org/

• About Intermine http://intermine.org/wiki/InterMine

• Intermine Overview http://intermine.org/wiki/InterMineOverview

• Prerequisite and downloading http://intermine.org/wiki/GettingStarted http://intermine.org/wiki/Prerequisites

• Hardware requirements http://intermine.org/wiki/Hardware

• QuickStart http://intermine.org/wiki/QuickStart

• TroubleShooting http://intermine.org/wiki/TroubleshootingTips

• Download/Get intermine http://intermine.org/wiki/SVNCheckout

• Intermine use cases http://intermine.org/wiki/InterMineUseCases

Examples of databases using Intermine

• RatMine: http://ratmine.mcw.edu/
• modENCODE: http://www.modencode.org/
• Flymine: http://www.flymine.org/
• Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do
• Targetmine : http://targetmine.nibio.go.jp/
• Metabolicmine : http://www.metabolicmine.org/

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 http://intermine.org/wiki/Prerequisites

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

3. Install ant

  a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/
  b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26
  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/startup.sh (to start the server)
  /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh  (to stop it)		
  Add a manager for tomcat by editing file  $CATALINA_HOME/conf/tomcat-users.xml   ($CATALINA_HOME is the installation directory)
  <tomcat-users>
  <role rolename="manager"/>
  <user username="manager" password="manager" roles="manager"/>
  </tomcat-users>

  Add java memmory requirements
  To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR
  Edit the file $TOMCAT_HOME/bin/startup.sh 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 http://intermine.org/wiki/Prerequisites
  sudo vim /etc/postgresql/8.4/main/postgresql.conf
  Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)
  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 http://www.bioinformatics.org/bioseg/wiki/   
  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 http://www.junit.org/
  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.
  like
  export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar

Step B: Download and Install Intermine

  svn co svn://subversion.flymine.org/branches/intermine_0_98
  Thats all :)

Step C: Creating a example database using Malaria called Malariamine.

  Please follow the steps given at http://intermine.org/wiki/GettingStarted