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1 #!/bin/sh -e
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2 #
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3 # Wrapper script to run weeder2 as a Galaxy tool
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4 #
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5 # Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE FREQFILES_DIR MOTIFS_OUT MATRIX_OUT [ ARGS... ]
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6 #
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7 # ARGS: one or more arguments to supply directly to weeder2
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8 #
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9 # Process command line
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10 FASTA_IN=$1
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11 SPECIES_CODE=$2
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12 FREQFILES_DIR=$3
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13 MOTIFS_OUT=$4
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14 MATRIX_OUT=$5
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15 #
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16 # Other arguments
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17 ARGS=""
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18 while [ ! -z "$6" ] ; do
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19 ARGS="$ARGS $6"
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20 shift
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21 done
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22 #
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23 # Link to input file
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24 ln -s $FASTA_IN
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25 #
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26 # Locate the FreqFiles directory
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27 if [ $FREQFILES_DIR == "." ] ; then
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1
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28 # Don't explicitly set the location - Weeder2 from
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29 # bioconda handles this automatically
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30 freqfiles_dir=
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0
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31 else
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32 # Alternative location
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33 freqfiles_dir=$FREQFILES_DIR
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34 fi
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35 #
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36 # Link to the FreqFiles directory as weeder2 executable
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37 # expects it to be the same directory
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1
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38 if [ ! -z "$freqfiles_dir" ] ; then
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39 if [ -d $freqfiles_dir ] ; then
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40 echo "Linking to FreqFiles directory: $freqfiles_dir"
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41 ln -s $freqfiles_dir FreqFiles
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42 else
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43 echo "ERROR FreqFiles directory not found" >&2
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44 exit 1
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45 fi
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0
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46 else
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1
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47 echo "WARNING FreqFiles directory not set" >&2
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0
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48 fi
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49 #
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50 # Construct names of input and output files
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1
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51 fasta=$(basename $FASTA_IN)
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52 motifs_out=${fasta}.w2
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53 matrix_out=${fasta}.matrix.w2
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0
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54 #
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55 # Construct and run weeder command
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56 # NB weeder logs output to stderr so redirect to stdout
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57 # to prevent the Galaxy tool reporting failure
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58 weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS"
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59 echo "Running $weeder_cmd"
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60 $weeder_cmd 2>&1
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61 status=$?
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62 if [ $status -ne 0 ] ; then
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63 echo weeder2 command finished with nonzero exit code $status >&2
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64 echo Command was: $weeder_cmd
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65 exit $status
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66 fi
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67 #
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68 # Move outputs to final destinations
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69 if [ -e $motifs_out ] ; then
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70 /bin/mv $motifs_out $MOTIFS_OUT
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1
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71 else
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72 echo ERROR missing output file: $motifs_out >&2
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73 status=1
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0
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74 fi
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75 if [ -e $matrix_out ] ; then
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76 /bin/mv $matrix_out $MATRIX_OUT
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1
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77 else
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78 echo ERROR missing output file: $matrix_out >&2
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79 status=1
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0
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80 fi
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81 #
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82 # Done
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1
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83 exit $status
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