testsrc/testdata/ljobs/Muscle#1485235375293604/RunnerConfig.xml

   1 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
   2 <runConfiguration>
   3     <taskId>Muscle#1485235375293604</taskId>
   4     <workDirectory>/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout/Muscle#1485235375293604</workDirectory>
   5     <parameters>
   6         <paramList>
   7             <entry>
   8                 <key>-clwstrict</key>
   9                 <value>
  10                     <position>-1</position>
  11                     <name>-clwstrict</name>
  12                 </value>
  13             </entry>
  14             <entry>
  15                 <key>-quiet</key>
  16                 <value>
  17                     <position>-1</position>
  18                     <name>-quiet</name>
  19                 </value>
  20             </entry>
  21             <entry>
  22                 <key>-verbose</key>
  23                 <value>
  24                     <position>-1</position>
  25                     <name>-verbose</name>
  26                 </value>
  27             </entry>
  28             <entry>
  29                 <key>-log</key>
  30                 <value>
  31                     <position>-1</position>
  32                     <name>-log</name>
  33                     <value>stat.log</value>
  34                 </value>
  35             </entry>
  36             <entry>
  37                 <key>-in</key>
  38                 <value>
  39                     <position>-1</position>
  40                     <name>-in</name>
  41                     <value>fasta.in</value>
  42                 </value>
  43             </entry>
  44             <entry>
  45                 <key>-out</key>
  46                 <value>
  47                     <position>-1</position>
  48                     <name>-out</name>
  49                     <value>fasta.out</value>
  50                 </value>
  51             </entry>
  52             <entry>
  53                 <key>-center</key>
  54                 <value>
  55                     <position>-1</position>
  56                     <name>-center</name>
  57                     <value>0.0</value>
  58                 </value>
  59             </entry>
  60             <entry>
  61                 <key>-matrix</key>
  62                 <value>
  63                     <position>-1</position>
  64                     <name>-matrix</name>
  65                     <value>/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/matrices/PAM10</value>
  66                 </value>
  67             </entry>
  68             <entry>
  69                 <key>-seqtype</key>
  70                 <value>
  71                     <position>-1</position>
  72                     <name>-seqtype</name>
  73                     <value>auto</value>
  74                 </value>
  75             </entry>
  76             <entry>
  77                 <key>-hydro</key>
  78                 <value>
  79                     <position>-1</position>
  80                     <name>-hydro</name>
  81                     <value>5</value>
  82                 </value>
  83             </entry>
  84             <entry>
  85                 <key>-weight2</key>
  86                 <value>
  87                     <position>-1</position>
  88                     <name>-weight2</name>
  89                     <value>clustalw</value>
  90                 </value>
  91             </entry>
  92             <entry>
  93                 <key>-weight1</key>
  94                 <value>
  95                     <position>-1</position>
  96                     <name>-weight1</name>
  97                     <value>clustalw</value>
  98                 </value>
  99             </entry>
 100             <entry>
 101                 <key>-gapopen</key>
 102                 <value>
 103                     <position>-1</position>
 104                     <name>-gapopen</name>
 105                     <value>-6.0</value>
 106                 </value>
 107             </entry>
 108             <entry>
 109                 <key>-cluster2</key>
 110                 <value>
 111                     <position>-1</position>
 112                     <name>-cluster2</name>
 113                     <value>upgmb</value>
 114                 </value>
 115             </entry>
 116             <entry>
 117                 <key>-cluster1</key>
 118                 <value>
 119                     <position>-1</position>
 120                     <name>-cluster1</name>
 121                     <value>upgma</value>
 122                 </value>
 123             </entry>
 124             <entry>
 125                 <key>-maxiters</key>
 126                 <value>
 127                     <position>-1</position>
 128                     <name>-maxiters</name>
 129                     <value>16</value>
 130                 </value>
 131             </entry>
 132             <entry>
 133                 <key>-hydrofactor</key>
 134                 <value>
 135                     <position>-1</position>
 136                     <name>-hydrofactor</name>
 137                     <value>1.2</value>
 138                 </value>
 139             </entry>
 140             <entry>
 141                 <key>-gapextend</key>
 142                 <value>
 143                     <position>-1</position>
 144                     <name>-gapextend</name>
 145                     <value>-1.0</value>
 146                 </value>
 147             </entry>
 148             <entry>
 149                 <key>-distance1</key>
 150                 <value>
 151                     <position>-1</position>
 152                     <name>-distance1</name>
 153                     <value>kmer6_6</value>
 154                 </value>
 155             </entry>
 156         </paramList>
 157         <nameValueSeparator> </nameValueSeparator>
 158     </parameters>
 159     <error>error.txt</error>
 160     <output>fasta.out</output>
 161     <input>/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout/Muscle#1485235375293604/fasta.in</input>
 162     <runnerClassName>compbio.runner.msa.Muscle</runnerClassName>
 163 </runConfiguration>