Intermine
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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. | 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. | ||
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− | + | == Web Resources (Links) == | |
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− | == Web Resources == | + | |
* http://intermine.org/wiki/Hardware | * http://intermine.org/wiki/Hardware | ||
* http://intermine.org/wiki/Prerequisites | * http://intermine.org/wiki/Prerequisites | ||
* http://intermine.org/wiki/GettingStarted | * http://intermine.org/wiki/GettingStarted | ||
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+ | |||
+ | |||
+ | == 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> | ||
+ | <!-- you can add more users or roles if needed --> | ||
+ | <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 | ||
+ | |||
+ | |||
+ | |||
+ | ---- |
Revision as of 17:38, 7 January 2012
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 (Links)
- http://intermine.org/wiki/Hardware
- http://intermine.org/wiki/Prerequisites
- http://intermine.org/wiki/GettingStarted
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