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1 #!/bin/bash
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2 ## use #!/bin/bash -x for debugging
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3
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4 ## Galaxy wrapper for MUMmer (nucmer/promer)
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5 ## Alex Bossers, CVI of Wageningen UR, NL
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6 ## alex_dot_bossers_at_wur_dot_nl
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7 ##
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8 ## Sep 2010
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9 ##
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10 ## Wrapper runs MUMmer nucmer/promer and additional args
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11 ## Calculates the comparison scores (delta and optional coords file)
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12 ## Generates the optional STATIC comparison mummerplot to png (from delta file)
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13 ##
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14 ## finally the script renames (optional) output files to outfiles expected by Galaxy
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15 ##
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16 ##
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17 ## INPUT args:
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18 ## nucmer_tool.sh $input_ref $input_query $out_delta $out_coords $out_png $logfile
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19 ## @0 @1 @2 @3 @4 @5
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20 ## $algorithm $keep_delta $make_coords $keep_log $make_image $cmd_extra
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21 ## @6 @7 @8 @9 @10 @11
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22 ##
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23
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24 # Function to send error messages.
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25 log_err() { echo "$@" 1>&2; }
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26 # path to where mummer suite is installed
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27 # adjust this for your machine
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28 # If mummer is available in system path, leave empty
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29 # when using different path make sure the trailing slash is added.
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30 # mum_path = /opt/Mummer23/Mummer/
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31 mum_path=""
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32 tmp_path="/tmp/mummertmp/"
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33
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34 if [ $num_path"$(which mummer)" == "" ] && [ "$num_path" == "" ]; then
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35 log_err "mummer is not available in system path and not declarated in mum_path. Please install mummer."
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36 exit 127
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37 fi
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38
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39 # since we have more than 9 arguments we need to shift the sections or use own array
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40 args=("$@")
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41 # to keep things readible assign vars
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42 input_ref="${args[0]}"
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43 input_query="${args[1]}"
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44 out_delta="${args[2]}"
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45 out_coords="${args[3]}"
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46 out_png="${args[4]}"
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47 logfile="${args[5]}"
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48 algorithm="${args[6]}"
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49 keep_delta="${args[7]}"
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50 make_coords="${args[8]}"
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51 keep_log="${args[9]}"
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52 make_image="${args[10]}"
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53 cmd_extra="${args[11]}"
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54
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55 [ -d $tmp_path ] || mkdir $tmp_path
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56 cd $tmp_path
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57
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58 # enable/disable the STDOUT log file
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59 if [ "$keep_log" == "yes" ]; then
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60 logfile_c="2>$logfile"
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61 logfile_a="2>>$logfile"
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62 else
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63 #dump to dev/null
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64 logfile_c="2>&-"
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65 logfile_a="2>&-"
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66 fi
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67
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68 # extra mummer cmd line options
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69
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70 ## generate coords file on the fly?
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71 if [ "$make_coords" == "yes" ]; then
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72 options=" --coords"
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73 fi
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74 ## extra cmd line args to be concatenated in options? We need to prevent extra spaces!
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75 if [ "$cmd_extra" != "" ]; then
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76 if [ "$options" == "" ]; then
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77 options=" $cmd_extra"
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78 else
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79 options="$options $cmd_extra"
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80 fi
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81 fi
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82
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83 # run nucmer/promer
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84 # May only run Promer and Nucmer
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85 echo $algorithm
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86 if [[ $algorithm =~ ...mer$ ]]; then
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87 eval "$mum_path$algorithm$options $input_ref $input_query $logfile_c"
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88 else
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89 log_err 'ERROR, algorithm does not conform to ...mer'
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90 exit 1
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91 fi
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92
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93
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94 ## generate large png if option make_image = yes
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95 ## suppress error from mummerplot since some is deprecated but not a real error
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96 ## error can be easily avoided by modifying the source of mummerplot... just in case
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97 ## however we need to check if a valid png was generated. This is not the case is alignment is none
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98 ## 1 is stderr and 2 stdout. redirect to dev/null
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99 if [ "${make_image}" == "yes" ]; then
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100 eval "$mum_path mummerplot --large --png out.delta 1>&- $logfile_a"
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101 if [ -f "out.png" ]; then
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102 mv out.png $out_png
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103 #cleanup temp gnuplot file
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104 rm out.gp
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105 else
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106 log_err "not exist the req png file!"
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107 exit 1
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108 fi
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109
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110 ## clean up remaining files
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111 rm out.fplot
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112 rm out.rplot
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113
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114 fi
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115
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116 # keep/rename or delete delta file
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117 if [ "$keep_delta" == "yes" ]; then
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118 mv out.delta "$out_delta"
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119 else
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120 rm out.delta
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121 fi
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122
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123 # keep/rename coords file if it was created
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124 if [ "$make_coords" == "yes" ]; then
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125 mv out.coords "$out_coords"
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126 fi
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127 # end script
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128 exit 0 |
