trunk/htsworkflow/pipelines/test/testdata/gerald_config_0.2.6.xml

   1 <RunParameters>
   2 <ChipWideRunParameters>
   3   <ANALYSIS>default</ANALYSIS>
   4   <BAD_LANES></BAD_LANES>
   5   <BAD_TILES></BAD_TILES>
   6   <CONTAM_DIR></CONTAM_DIR>
   7   <CONTAM_FILE></CONTAM_FILE>
   8   <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
   9   <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
  10   <ELAND_REPEAT></ELAND_REPEAT>
  11   <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
  12   <EMAIL_LIST>diane</EMAIL_LIST>
  13   <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
  14   <EXPT_DIR>/home/diane/gec/080416_HWI-EAS229_0024_207BTAAXX/Data/C1-33_Firecrest1.8.28_19-04-2008_diane/Bustard1.8.28_19-04-2008_diane</EXPT_DIR>
  15   <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
  16   <FORCE>1</FORCE>
  17   <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
  18   <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
  19   <HAMSTER_FLAG>genome</HAMSTER_FLAG>
  20   <OUT_DIR>/home/diane/gec/080416_HWI-EAS229_0024_207BTAAXX/Data/C1-33_Firecrest1.8.28_19-04-2008_diane/Bustard1.8.28_19-04-2008_diane/GERALD_19-04-2008_diane</OUT_DIR>
  21   <POST_RUN_COMMAND></POST_RUN_COMMAND>
  22   <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
  23   <PURE_BASES>12</PURE_BASES>
  24   <QF_PARAMS>'((CHASTITY&gt;=0.6))'</QF_PARAMS>
  25   <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
  26   <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
  27   <READ_LENGTH>32</READ_LENGTH>
  28   <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
  29   <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
  30   <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
  31   <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
  32   <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
  33   <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
  34   <TILE_ROOT>s</TILE_ROOT>
  35   <TIME_STAMP>Sat Apr 19 19:08:30 2008</TIME_STAMP>
  36   <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
  37   <USE_BASES>all</USE_BASES>
  38   <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
  39 </ChipWideRunParameters>
  40 <LaneSpecificRunParameters>
  41   <ANALYSIS>
  42     <s_1>eland</s_1>
  43     <s_2>eland</s_2>
  44     <s_3>eland</s_3>
  45     <s_4>eland</s_4>
  46     <s_5>eland</s_5>
  47     <s_6>eland</s_6>
  48     <s_7>eland</s_7>
  49     <s_8>eland</s_8>
  50   </ANALYSIS>
  51   <ELAND_GENOME>
  52     <s_1>/g/dm3</s_1>
  53     <s_2>/g/equcab1</s_2>
  54     <s_3>/g/equcab1</s_3>
  55     <s_4>/g/canfam2</s_4>
  56     <s_5>/g/hg18</s_5>
  57     <s_6>/g/hg18</s_6>
  58     <s_7>/g/hg18</s_7>
  59     <s_8>/g/hg18</s_8>
  60   </ELAND_GENOME>
  61   <READ_LENGTH>
  62     <s_1>32</s_1>
  63     <s_2>32</s_2>
  64     <s_3>32</s_3>
  65     <s_4>32</s_4>
  66     <s_5>32</s_5>
  67     <s_6>32</s_6>
  68     <s_7>32</s_7>
  69     <s_8>32</s_8>
  70   </READ_LENGTH>
  71   <USE_BASES>
  72     <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
  73     <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
  74     <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
  75     <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
  76     <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
  77     <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
  78     <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
  79     <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
  80   </USE_BASES>
  81 </LaneSpecificRunParameters>
  82 </RunParameters>