<opt
  name="site_defaults"
  ROOT="${GMOD_ROOT}/"
  datadir="data/genomes"
  ftp_url="ftp://ftp.mygenome.org/genome"
  web_url="http://www.mygenome.org/genome"
>
  <title>Site Default settings for GMODTools</title>

  <about id="site_defaults">
  This is a configuration file for GMODTools Bulkfiles
  which can be included into data release configuration
  files.  Enter common settings, include other portions
  of the configurations settings here.  
  
  Simple tags that go well here:
    ROOT = where the base path for data is
    datadir = sub directory from ROOT
    ftp_url, web_url = used in output documents
    verbose = show these 'about' comments.
  
  Using 'include' options in the xml configurations will
  add these to main configuration, but not replace main
  settings.  Includes can be nested.
  </about>

  <db
    driver="Pg"
    name="${CHADO_DB_NAME}"
    host="${CHADO_DB_HOST}"
    port="${CHADO_DB_PORT}" 
    user="${CHADO_DB_USERNAME}"
    password="${CHADO_DB_PASSWORD}"
    />
  <about id="db"
    driver="Pg"
    name="chado_release_db"
    host="localhost"
    port="5432" 
    user=""
    password=""
    >
  This is an example setting for database access.
  If your system defines the values in gmod.conf, they
  will be used. If you dont use thse CHADO_ from gmod.conf,
  change above db settings.
  </about>


    <!-- or use bulkfiles defaults/user choice -->
  <outformats>overview</outformats>
  <outformats>fff</outformats>
  <outformats>gff</outformats>
  <outformats>fasta</outformats>
  <outformats>tables</outformats>
  <outformats>go_association</outformats>
  <outformats>blast</outformats>
  <about id="outformats" >
  ARRAY of default output files. Generally each of
  these has a Bulkfiles::BulkWriter perl subclass,
  and xml configuration.   fileset details these, including
  the Perl handler.
  </about>
  
  <doc id="Release.txt"><![CDATA[
  Bulk output for Chado genome databases
  Database: ${title}
  Species:  ${species}
  Release:  ${release_id}, dated ${release_date} as ${relfull}
  
  See release notes at <a href="${release_url}"> ${release_url}</a>
  ]]></doc>
  
  <about id="doc">
    doc tags are generally printed to files
    id= name, file name unless path given
    path= path to output file.
    A few common tags can be used as inserted ${variables}
  </about>

  <relfull>${org}_${release_date}</relfull> <!-- or ${org}_release${release_id} -->
  <release_url>/genome/${species}/release${release_id}.html</release_url>

  <newuser>1</newuser>
  <about id="newuser">
    This flag turns on extra help and checks.  Set 0 if you are tired
    of seeing them, or the time they take.
  </about>
  
  <include>organisms</include>
  <about id="organisms" >
  List of species and their abbreviations. Include your species.
  </about>
  
  <!-- how to make bulk files -->
  <include>filesets</include>
  <about id="filesets" >
  How to make bulk files.
  </about>

  <!-- feature sets to make fasta bulk files -->
  <include>featuresets</include>
  <about id="featuresets" >
  What feature sets for bulk files (esp. fasta sequence)
  and how they are grouped from primary features.
  </about>

</opt>
