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1 #!/bin/sh
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2
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3 ## This script creates a config file for use with the QDNAseq R wrapper
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4 ## For use outside Galaxy
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5
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6 QDNASEQ_R_SCRIPT='/ccagc/home/stef/code/QDNASEQ/QDNAseq.R'
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7 R_LOCATION='/ccagc/lib/R/R-3.1.0/bin/'
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8 OUTPUT_DIR='QDNASEQ'
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9 SCRIPT_DIR=$(dirname $0)
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10 SCRIPT_NAME=$(basename $0)
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11
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12 binSizesString='1000,100,15'
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13 outputName=`basename $PWD`
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14 doSegment='TRUE'
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15 debug='FALSE'
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16
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17 usage()
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18 {
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19 cat<<EOF
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20 This script creates a QDNAseq wrapper config.
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21
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22 Experiment name and/or output dir are optional
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23 $SCRIPT_NAME [-n myExperiment] [-o outputDir] *.bam
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24
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25 Debug mode for working with build in LGG150 data
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26 $SCRIPT_NAME -d
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27
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28 OPTIONS:
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29 -n [s] provide analysis name [$outputName]
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30 -o [s] output dir [$OUTPUT_DIR]
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31 -d debug mode (only create config)
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32
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33 EOF
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34 }
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35
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36 PARAM_COUNT=0
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37 if [ $# -eq 0 ] || [ "$1" == "-h" ]
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38 then
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39 usage
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40 exit 1
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41 else
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42 while getopts "n:o:d" opt; do
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43 case $opt in
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44 n)
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45 #echo "$opt was triggered, Parameter: $OPTARG" >&2
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46 outputName=$OPTARG
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47 PARAM_COUNT=`bc <<< $PARAM_COUNT+2`
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48 ;;
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49 o)
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50 OUTPUT_DIR=$OPTARG
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51 PARAM_COUNT=`bc <<< $PARAM_COUNT+2`
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52 ;;
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53 d)
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54 debug='TRUE'
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55 PARAM_COUNT=`bc <<< $PARAM_COUNT+1`
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56 ;;
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57 \?)
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58 echo "Invalid option: -$OPTARG" >&2
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59 exit 1
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60 ;;
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61 :)
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62 echo "Option -$OPTARG requires an argument." >&2
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63 exit 1
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64 ;;
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65 esac
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66 done
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67 fi
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68
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69 ## set param dependent variables
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70 printf '%s\n' "[INFO] --- QDNAseq wrapper config creator ---"
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71 CONFIG_FILE=$OUTPUT_DIR'/qdnaseqConfig.R'
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72
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73 ## remove the params from input string leaving only the BAMs
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74 shift $PARAM_COUNT
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75
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76 ## sanity checks
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77 if [ -e $CONFIG_FILE ]; then
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78 echo "[ERR] Config file ($CONFIG_FILE) already exists, exit..";
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79 exit 0
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80 fi
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81 if [ -d $OUTPUT_DIR ]; then
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82 echo "[ERR] Output dir ($OUTPUT_DIR) already exists, exit..";
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83 exit 0
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84 else
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85 mkdir $OUTPUT_DIR
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86 fi
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87
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88 ## variables setup
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89 CONFIG_TXT="## ==========
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90 ## QDNAseq pipeline config file
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91 ## ==========
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92
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93 ## ----------
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94 inGalaxy <- FALSE
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95 binSizesString <- '$binSizesString'
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96 experimentType <- 'SR50'
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97 outputName <- '$outputName'
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98
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99 ## ----------
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100 outputHtml <- 'galaxyIndex.html'
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101 outputId <- NA
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102 newFilePath <- '$OUTPUT_DIR'
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103 outputPath <- '$OUTPUT_DIR'
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104 doSegment <- as.logical( $doSegment )
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105 debug <- as.logical( $debug )
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106 undoSD <- as.double( 1.0 )
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107 binAnnotations <- ''
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108
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109 ## ----------
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110 filterBlacklistedBins <- as.logical( 'TRUE' )
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111 mappabilityCutoff <- as.integer( 0 )
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112 undoSplits <- 'sdundo'
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113 doOutputCopynumbersIgv <- FALSE
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114
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115 ## ----------
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116 PLOT_WIDTH <- as.integer( 1440 )
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117 PLOT_HEIGHT <- as.integer( 720 )
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118 excludeChrsString <- 'X,Y'
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119
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120 ## ----------
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121 bamsPaths <- c()
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122 bamsNames <- c()
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123 "
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124
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125 ## create config file
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126 printf '%s\n' "$CONFIG_TXT" > $CONFIG_FILE
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127
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128 ## add bam files to config file
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129 BAMS=$@
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130 for bam_path in $BAMS; do
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131
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132 if [ ! -e $bam_path ]; then
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133 echo "[ERR] Bam file does not exist ($bam_path), exit..";
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134 exit 0
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135 fi
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136
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137 bam_name=`basename "$bam_path"`
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138 printf '%s\n' "bamsPaths <- c( bamsPaths, \"$bam_path\" )" >> $CONFIG_FILE
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139 printf '%s\n' "bamsNames <- c( bamsNames, \"$bam_name\" )" >> $CONFIG_FILE
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140 printf '%s\n' "[INFO] BAM: $bam_name"
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141 done
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142
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143 ## done
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144 printf '%s\n' "[INFO] OUTPUT DIR: $OUTPUT_DIR"
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145 printf '%s\n' "[INFO] OUTPUT NAME: $outputName"
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146 printf '%s\n' "[INFO] CONFIG FILE can be found in $CONFIG_FILE"
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147 printf '%s\n' "[INFO] Run with: $R_LOCATION/Rscript $QDNASEQ_R_SCRIPT $CONFIG_FILE"
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148 printf '%s\n' "[INFO] Done" |
