RTG Galaxy tools
----------------

Install:

Copy lib/galaxy/datatypes/rtg.py and the tools/rtg directory to the same locations in your galaxy distribution.

Then edit the following files:

galaxy_dist/tools/rtg/rtg-galaxy.cfg

  change the rtg variable to point at the rtg file in your RTG installation directory
    
galaxy_dist/lib/galaxy/datatypes/registry.py
  add
    , rtg
  to the list of imports beginning with data, tabular, interval...


galaxy_dist/tool_conf.xml
  Within the <toolbox> node, add
  
  <section name="Realtime Genomics" id="rtg">
    <label text="Data formatting" id="formatting" />
    <tool file="rtg/format_fasta.xml" />
    <tool file="rtg/format_fastq.xml" />
    <tool file="rtg/cg2sdf.xml" />
    <tool file="rtg/sdf2fasta.xml" />
    <label text="Read mapping" id="mapping" />
    <tool file="rtg/map.xml" />
    <tool file="rtg/cgmap.xml" />
    <tool file="rtg/mapf.xml" />
    <tool file="rtg/mapx.xml" />
    <label text="Variant detection" id="variant" />
    <tool file="rtg/snp.xml" />
    <tool file="rtg/coverage.xml" />
    <tool file="rtg/snpintersection.xml" />
    <label text="Simulation" id="sim" />
    <tool file="rtg/genomesim.xml" />
    <tool file="rtg/cgsim.xml" />
    <tool file="rtg/readsim.xml" />
    <tool file="rtg/snpsim.xml" />
  </section>

galaxy_dist/datatypes_config.xml
  Within the <datatypes><registration> node, add
  
        <!-- Start RTG Datatypes -->
        <datatype extension="rtg_sdf" type="galaxy.datatypes.rtg:Sdf"/>
        <datatype extension="tsvcg" type="galaxy.datatypes.rtg:Cgtsv" display_in_upload="true"/>
        <datatype extension="samix" type="galaxy.datatypes.rtg:Samix" display_in_upload="true"/>
        <!-- End RTG Datatypes -->

  Within the <datatypes><sniffers> node, add
        <sniffer type="galaxy.datatypes.rtg:Samix"/>
        <sniffer type="galaxy.datatypes.rtg:Cgtsv"/>