source: trunk/bio/tutorial/malariamine/project.xml @ 23419

<project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="source.location" location="../bio/sources/"/>
  <property name="source.location" location="../bio/sources/example-sources/"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="malariamine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>

  <sources>
    <source name="uniprot-malaria" type="uniprot">
      <property name="uniprot.organisms" value="36329"/>
      <property name="createinterpro" value="true"/>
      <property name="creatego" value="true"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/uniprot/"/>
    </source>
    <source name="malaria-gff" type="malaria-gff">
      <property name="gff3.taxonId" value="36329"/>
      <property name="gff3.seqDataSourceName" value="PlasmoDB"/>
      <property name="gff3.dataSourceName" value="PlasmoDB"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="PlasmoDB P. falciparum genome"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/genome/gff"/>
    </source>
    <source name="malaria-chromosome-fasta" type="fasta" dump="true">
      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="PlasmoDB"/>
      <property name="fasta.dataSetTitle" value="PlasmoDB chromosome sequence"/>
      <property name="fasta.taxonId" value="36329"/>
      <property name="fasta.includes" value="MAL*.fasta"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/genome/fasta"/>
    </source>
    <source name="interpro" type="interpro">
      <property name="src.data.dir" location="DATA_DIR/malaria/interpro"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="DATA_DIR/malaria/go/gene_ontology.obo"/>
      <property name="createrelations" value="false"/>
    </source>
    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="DATA_DIR/malaria/go/gene_ontology.obo"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/go-annotation/"/>
    </source>
    <source name="update-publications" type="update-publications">
      <property name="src.data.file" location="build/publications.xml"/>
    </source>
    <source name="entrez-organism" type="entrez-organism">
      <property name="src.data.file" location="build/organisms.xml"/>
    </source>
  </sources>

  <post-processing>
    <post-process name="create-references"/>
    <post-process name="transfer-sequences" dump="true"/>

    <!-- this runs the postprocessing steps in all sources -->
    <post-process name="do-sources"/>

    <post-process name="summarise-objectstore"/>
    <post-process name="create-autocomplete-index"/>
    <post-process name="create-search-index"/>
  </post-processing>

</project>