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1 #!/bin/bash
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2
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3 ## simple bash to generate mummerplot of MATCH file
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4 ##
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5 ## Galaxy wrapper by Alex Bossers, CVI of Wageningen UR, Lelystad, NL
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6 ## alex_dot_bossers_at_wur_dot_nl
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7 ##
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8 ##
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9 ## needs a rename of the fixed name to something recognised by galaxy
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10 ## needs cleanout of temp files
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11 ##
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12 ## call is mummerplot $format $in_match $out_file $cmd_extra
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13 ## $0 $1 $2 $3 $4
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14 ##
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15 ## since mummerplot uses some deprecated syntax which can be fixed in the source
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16 ## we redirect STDERR to dev/null to circumvent errorstatus in galaxy
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17 ## io redirects 0=stdin 1=stdout 2=stderr to dev/null (or &-)
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18
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19 # Function to send error messages.
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20 log_err() { echo "$@" 1>&2; }
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21
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22 # path to where mummer suite is installed
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23 # adjust this for your machine
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24 # this is the only hard coded path in the scripts
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25 mum_path=""
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26
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27 if [ $num_path"$(which mummer)" == "" ] && [ "$num_path" == "" ]; then
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28 log_err "mummer is not available in system path and not declarated in mum_path. Please install mummer."
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29 exit 127
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30 fi
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31
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32 # some default options to generate a LARGE fixed PNG/POSTSCRIPT image and not an interactive one.
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33
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34 if [ "$1" = "png" ]; then
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35 extension="png"
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36 else
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37 extension="ps"
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38 fi
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39
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40 eval "$mum_path mummerplot --large --$1 $2 1>&- 2>&-"
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41 if [ -f "out.$extension" ]; then
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42 #conditional move to something known by galaxy
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43 mv out.$extension $3
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44 #remove gnuplot file
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45 rm out.gp
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46 fi
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47
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48 ## clean up
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49 rm out.fplot
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50 rm out.rplot
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51
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52 #end script
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