We have looked at various InterMine sources used in MalariaMine and seen how to create a new source from scratch. Finally we will look at a script used to build a Mine in a single step.

Building a Mine

So far we have created databases, integrated data and run post-processing with individual ant targets. InterMine includes a perl program called project_build that reads the project.xml definition and runs all of the steps in sequence. It also has the option of dumping the production database during the build and recovering from these dumps in case of problems.

See this page for full documentation: RunningABuild

Build complete MalariaMine

Build MalariaMine now using the project_build script, we will need a completed MalariaMine for the webapp tutorials on day two.

• Make sure your working KEGG source is included in project.xml
• If your own KEGG source isn't completed you can use the kegg-example source instead:

  <source name="kegg-example" type="kegg-example">
    <property name="taxonId" value="36329"/>
    <property name="src.data.dir" location="DATA_DIR/malaria/kegg/"/>
  </source>  
  

• Run the project_build script from your malariamine directory:

  ../bio/scripts/project_build -b -t -v localhost ~/malariamine-dump
  

  This will take ~15mins to complete.

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You should now have a complete MalariMine with several data sources loaded. On day two we will release and configure web application to access this data.

Next: Workshop