Mercurial > repos > kuyt002 > mummer_toolsuite
comparison MUMmer/mummer_tool.sh @ 0:61f30d177448 default tip
initial commit on Mummer toolsuite on toolshed
| author | eric |
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| date | Tue, 31 Mar 2015 14:19:49 +0200 |
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| -1:000000000000 | 0:61f30d177448 |
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| 1 #!/bin/bash | |
| 2 ## use #!/bin/bash -x for debugging | |
| 3 | |
| 4 ## Galaxy wrapper for MUMmer (nucmer/promer) | |
| 5 ## Alex Bossers, CVI of Wageningen UR, NL | |
| 6 ## alex_dot_bossers_at_wur_dot_nl | |
| 7 ## | |
| 8 ## Sep 2010 | |
| 9 ## | |
| 10 ## Wrapper runs MUMmer nucmer/promer and additional args | |
| 11 ## Calculates the comparison scores (delta and optional coords file) | |
| 12 ## Generates the optional STATIC comparison mummerplot to png (from delta file) | |
| 13 ## | |
| 14 ## finally the script renames (optional) output files to outfiles expected by Galaxy | |
| 15 ## | |
| 16 ## | |
| 17 ## INPUT args: | |
| 18 ## nucmer_tool.sh $input_ref $input_query $out_delta $out_coords $out_png $logfile | |
| 19 ## @0 @1 @2 @3 @4 @5 | |
| 20 ## $algorithm $keep_delta $make_coords $keep_log $make_image $cmd_extra | |
| 21 ## @6 @7 @8 @9 @10 @11 | |
| 22 ## | |
| 23 | |
| 24 # Function to send error messages. | |
| 25 log_err() { echo "$@" 1>&2; } | |
| 26 # path to where mummer suite is installed | |
| 27 # adjust this for your machine | |
| 28 # If mummer is available in system path, leave empty | |
| 29 # when using different path make sure the trailing slash is added. | |
| 30 # mum_path = /opt/Mummer23/Mummer/ | |
| 31 mum_path="" | |
| 32 tmp_path="/tmp/mummertmp/" | |
| 33 | |
| 34 if [ $num_path"$(which mummer)" == "" ] && [ "$num_path" == "" ]; then | |
| 35 log_err "mummer is not available in system path and not declarated in mum_path. Please install mummer." | |
| 36 exit 127 | |
| 37 fi | |
| 38 | |
| 39 # since we have more than 9 arguments we need to shift the sections or use own array | |
| 40 args=("$@") | |
| 41 # to keep things readible assign vars | |
| 42 input_ref="${args[0]}" | |
| 43 input_query="${args[1]}" | |
| 44 out_delta="${args[2]}" | |
| 45 out_coords="${args[3]}" | |
| 46 out_png="${args[4]}" | |
| 47 logfile="${args[5]}" | |
| 48 algorithm="${args[6]}" | |
| 49 keep_delta="${args[7]}" | |
| 50 make_coords="${args[8]}" | |
| 51 keep_log="${args[9]}" | |
| 52 make_image="${args[10]}" | |
| 53 cmd_extra="${args[11]}" | |
| 54 | |
| 55 [ -d $tmp_path ] || mkdir $tmp_path | |
| 56 cd $tmp_path | |
| 57 | |
| 58 # enable/disable the STDOUT log file | |
| 59 if [ "$keep_log" == "yes" ]; then | |
| 60 logfile_c="2>$logfile" | |
| 61 logfile_a="2>>$logfile" | |
| 62 else | |
| 63 #dump to dev/null | |
| 64 logfile_c="2>&-" | |
| 65 logfile_a="2>&-" | |
| 66 fi | |
| 67 | |
| 68 # extra mummer cmd line options | |
| 69 | |
| 70 ## generate coords file on the fly? | |
| 71 if [ "$make_coords" == "yes" ]; then | |
| 72 options=" --coords" | |
| 73 fi | |
| 74 ## extra cmd line args to be concatenated in options? We need to prevent extra spaces! | |
| 75 if [ "$cmd_extra" != "" ]; then | |
| 76 if [ "$options" == "" ]; then | |
| 77 options=" $cmd_extra" | |
| 78 else | |
| 79 options="$options $cmd_extra" | |
| 80 fi | |
| 81 fi | |
| 82 | |
| 83 # run nucmer/promer | |
| 84 # May only run Promer and Nucmer | |
| 85 echo $algorithm | |
| 86 if [[ $algorithm =~ ...mer$ ]]; then | |
| 87 eval "$mum_path$algorithm$options $input_ref $input_query $logfile_c" | |
| 88 else | |
| 89 log_err 'ERROR, algorithm does not conform to ...mer' | |
| 90 exit 1 | |
| 91 fi | |
| 92 | |
| 93 | |
| 94 ## generate large png if option make_image = yes | |
| 95 ## suppress error from mummerplot since some is deprecated but not a real error | |
| 96 ## error can be easily avoided by modifying the source of mummerplot... just in case | |
| 97 ## however we need to check if a valid png was generated. This is not the case is alignment is none | |
| 98 ## 1 is stderr and 2 stdout. redirect to dev/null | |
| 99 if [ "${make_image}" == "yes" ]; then | |
| 100 eval "$mum_path mummerplot --large --png out.delta 1>&- $logfile_a" | |
| 101 if [ -f "out.png" ]; then | |
| 102 mv out.png $out_png | |
| 103 #cleanup temp gnuplot file | |
| 104 rm out.gp | |
| 105 else | |
| 106 log_err "not exist the req png file!" | |
| 107 exit 1 | |
| 108 fi | |
| 109 | |
| 110 ## clean up remaining files | |
| 111 rm out.fplot | |
| 112 rm out.rplot | |
| 113 | |
| 114 fi | |
| 115 | |
| 116 # keep/rename or delete delta file | |
| 117 if [ "$keep_delta" == "yes" ]; then | |
| 118 mv out.delta "$out_delta" | |
| 119 else | |
| 120 rm out.delta | |
| 121 fi | |
| 122 | |
| 123 # keep/rename coords file if it was created | |
| 124 if [ "$make_coords" == "yes" ]; then | |
| 125 mv out.coords "$out_coords" | |
| 126 fi | |
| 127 # end script | |
| 128 exit 0 |