mkdir -p '$jbrowse.files_path/'

&&


      if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then
        echo "__default: local" > '.auth.yml' &&
        echo "local:" >> '.auth.yml' &&
        echo "    url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' &&
        echo "    username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' &&
        echo "    password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' &&

        export ARROW_GLOBAL_CONFIG_PATH='.auth.yml'
      ; fi &&
  

python '$__tool_directory__/fetch_organism_jbrowse.py'



#if $org_source.source_select == "auto_json":
    --org_json '${org_source.org_file}'
#elif $org_source.source_select == "select":
    --org_id '${org_source.org_select}'
#else:
    --org_raw '${org_source.org_raw}'
#end if

  
'$jbrowse.files_path/'

'$__user_email__' &&

cp '$dummyIndex' '$jbrowse' &&
find '$jbrowse.files_path' -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse &&
echo '</ul></body></html>' >> '$jbrowse'