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1 #!/bin/sh -e
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2 #
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3 # Wrapper script to run CEASbw as a Galaxy tool
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4 #
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5 # Usage: ceasbw_wrapper.sh $BED_IN $GDB_IN $EXTRA_BED_IN $LOG_OUT $PDF_OUT $XLS_OUT $DBKEY
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6 #
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7 # Process command line
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8 echo $*
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9 BED_IN=$1
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10 GDB_IN=$2
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11 EXTRA_BED_IN=$3
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12 LOG_OUT=$4
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13 PDF_OUT=$5
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14 XLS_OUT=$6
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15 #
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16 # Collect remaining args
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17 CEAS=ceas
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18 OPTIONS=
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19 while [ ! -z "$7" ] ; do
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20 if [ "$7" == "--bigwig" ] ; then
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21 CEAS=ceasBW
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22 fi
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23 OPTIONS="$OPTIONS $7"
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24 shift
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25 done
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26 #
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27 # Convenience variables for local files
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28 base_name="ceas"
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29 log_file=${base_name}.log
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30 r_script=${base_name}.R
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31 pdf_report=${base_name}.pdf
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32 xls_file=${base_name}.xls
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33 #
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34 # Get CEAS version
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35 echo Running $CEAS
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36 $CEAS --version >$log_file 2>/dev/null
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37 #
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38 # Construct and run CEAS command line
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39 ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN"
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40 if [ "$EXTRA_BED_IN" != "None" ] ; then
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41 ceas_cmd="$ceas_cmd -e $EXTRA_BED_IN"
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42 fi
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43 echo "Running $ceas_cmd"
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44 $ceas_cmd >>$log_file 2>&1
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45 #
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46 # Move outputs to final destination
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47 if [ -e $log_file ] ; then
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48 echo "Moving $log_file to $LOG_OUT"
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49 /bin/mv $log_file $LOG_OUT
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50 else
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51 echo ERROR failed to make log file >&2
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52 exit 1
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53 fi
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54 if [ -e $xls_file ] ; then
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55 echo "Moving $xls_file to $XLS_OUT"
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56 /bin/mv $xls_file $XLS_OUT
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57 else
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58 echo ERROR failed to generate XLS file >&2
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59 exit 1
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60 fi
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61 #
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62 # Run the R script to generate the PDF report
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63 if [ -e $r_script ] ; then
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64 echo "Running $r_script to generate $pdf_report"
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65 R --vanilla < $r_script
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66 if [ -e $pdf_report ] ; then
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67 echo "Moving $xls_file to $XLS_OUT"
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68 /bin/mv $pdf_report $PDF_OUT
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69 else
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70 echo ERROR failed to generate PDF report >&2
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71 exit 1
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72 fi
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73 else
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74 echo ERROR no R script to generate PDF report >&2
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75 exit 1
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76 fi
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77 #
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78 # Done
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