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    </item>

  </bundle>
  
  <bundle name="External applications">

    <item installed="false" name="ClusterBuster" type="application">
      <dir>/opt/chipster/tools/ClusterBuster</dir>
      <comment>
      	Download http://zlab.bu.edu/~mfrith/downloads/cbust-src.tar.gz and install.
      </comment>
    </item>
    
	<item installed="false" name="Jaspar motif collection" type="application">
	  <dir>/opt/chipster/tools/ClusterBuster</dir>
	  <comment>
	  	Download from http://zlab.bu.edu/clover/jaspar2 file jaspar2005core.txt.
	  </comment>
	</item>

    <item installed="false" name="Weeder" type="application">
      <dir>/opt/chipster/tools/weeder</dir>
      <comment>
      	Download http://159.149.109.9/modtools/downloads/weeder1.3.1.tar.gz 
      	and install.
      </comment>
    </item>

	<item installed="false" name="Promoter sequences" type="application">
	  <dir>/opt/chipster/tools/weeder/seqs</dir>
      <comment>	
      	Promoter analysis tools need the promoter sequences in a suitable format. 
      	Download and unpack sequence files to directory weeder/seqs: 
      	http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/tools_extras/weeder-seqs/all-sequence-files.zip
        For information on how the sequence files were generated, see 
        http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/tools_extras/weeder-seqs/README.TXT 
      </comment>
    </item>

  </bundle>

</environment>
