annotate ceas_wrapper.sh @ 4:cd6a48ffd093 draft default tip

Uploaded version 1.0.2-4.
author pjbriggs
date Wed, 26 Sep 2018 08:03:10 -0400
parents f411ce97a351
children
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1 #!/bin/sh -e
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2 #
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3 # Wrapper script to run CEAS as a Galaxy tool
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4 #
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5 # This runs the Cistrome versions of CEAS, which provides two executables:
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6 # - ceas (same as the "official" version)
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7 # - ceasBW (modified version that accepts a bigwig file as input)
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8 #
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9 # Usage: ceas_wrapper.sh $BED_IN $GDB_IN $LOG_OUT $PDF_OUT $XLS_OUT [OPTIONS]
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10 #
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11 # Initialise
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12 CEAS=ceas
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13 #
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14 # Process command line
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15 echo $*
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16 BED_IN=$1
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17 GDB_IN=$2
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18 LOG_OUT=$3
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19 PDF_OUT=$4
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20 XLS_OUT=$5
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21 #
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22 # Initialise other variables
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23 EXTRA_BED_IN=
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24 #
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25 # Collect remaining args
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26 OPTIONS=
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27 while [ ! -z "$6" ] ; do
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28 if [ "$6" == "--bigwig" ] ; then
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29 # Bigwig input, need to use 'ceasBW'
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30 CEAS=ceasBW
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31 OPTIONS="$OPTIONS --bigwig"
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32 elif [ "$6" == "--length" ] ; then
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33 # Need a chrom sizes file
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34 chrom_sizes=$7
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35 if [ ! -f "$chrom_sizes" ] ; then
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36 # If chrom sizes file doesn't already exist then attempt to
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37 # download the data from UCSC
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38 echo "WARNING no file $chrom_sizes"
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39 dbkey=$(echo $(basename $chrom_sizes) | cut -d'.' -f1)
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40 if [ $dbkey == '?' ] ; then
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41 # DBkey not set, this is fatal
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42 echo "ERROR genome build not set, cannot get sizes for '?'" >&2
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43 echo "Assign a genome build to your input dataset and rerun" >&2
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44 exit 1
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45 fi
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46 # Fetch the sizes using fetchChromSizes
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47 echo -n "Attempting to download chromosome sizes for $dbkey..."
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48 chrom_sizes=$(basename $chrom_sizes)
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49 fetchChromSizes $dbkey >$chrom_sizes 2>/dev/null
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50 if [ $? -ne 0 ] ; then
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51 echo "failed"
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52 echo "ERROR unable to fetch data for ${dbkey}" >&2
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53 echo "Please check the genome build associated with your input dataset" >&2
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54 echo "or update your Galaxy instance to include an appropriate .len file" >&2
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55 exit 1
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56 else
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57 echo "ok"
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58 fi
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59 fi
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60 OPTIONS="$OPTIONS --length $chrom_sizes"
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61 shift
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62 else
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63 OPTIONS="$OPTIONS $6"
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64 fi
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65 shift
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66 done
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67 #
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68 # Convenience variables for local files
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69 base_name="ceas"
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70 log_file=${base_name}.log
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71 pdf_report=${base_name}.pdf
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72 xls_file=${base_name}.xls
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73 #
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74 # Get CEAS version
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75 echo Running $CEAS
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76 $CEAS --version >$log_file 2>/dev/null
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77 #
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78 # Construct and run CEAS command line
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79 ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN"
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80 echo "Running $ceas_cmd"
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81 $ceas_cmd >>$log_file 2>&1
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82 status=$?
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83 if [ $status -ne 0 ] ; then
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84 echo "Error: log file tail:"
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85 tail $log_file
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86 echo "ERROR $CEAS exited with non-zero code: $status" >&2
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87 exit $status
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88 fi
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89 #
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90 # Move outputs to final destination
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91 if [ -e $log_file ] ; then
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92 echo "Moving $log_file to $LOG_OUT"
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93 /bin/mv $log_file $LOG_OUT
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94 else
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95 echo ERROR failed to make log file >&2
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96 exit 1
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97 fi
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98 if [ -e $xls_file ] ; then
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99 echo "Moving $xls_file to $XLS_OUT"
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100 /bin/mv $xls_file $XLS_OUT
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101 else
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102 echo ERROR failed to generate XLS file >&2
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103 exit 1
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104 fi
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105 if [ -e $pdf_report ] ; then
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106 echo "Moving $pdf_report to $PDF_OUT"
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107 /bin/mv $pdf_report $PDF_OUT
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108 else
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109 echo ERROR failed to generate PDF report >&2
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110 exit 1
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111 fi
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112 #
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113 # Done