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2
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1 #!/bin/bash
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2 TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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3
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4 echo "Start falco sh"
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5
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6 ## ----------
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7 ## Variables setup
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8 ## ----------
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9 #bam_file=$1
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10 #bam_name=$2
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11 #html_out=$3
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12 #vcf_out=$4
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13 #out_path=$5
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14 source $1
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15
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16 bam_base=`echo $bam_name | sed 's#.bam$##' - `
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17
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18 ## ----------
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19 ## Create extra init script
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20 ## ----------
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21 #if [ $design_file != 'None' && $design_file != '' ]; then BED_PATH=$design_file; fi
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22 #if [ $manifest_file != 'None' && $manifest_file != '' ]; then MAN_PATH=$manifest_file; fi
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23 if [ $design_file != 'None' ] # Galaxy default is "None"
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24 then
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25 BED_PATH=$design_file
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26 else
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27 BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed"
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28 fi
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29
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30 if [ $manifest_file != 'None' ] # Galaxy default is "None"
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31 then
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32 MAN_PATH=$manifest_file
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33 else
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34 MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"
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35 fi
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36
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37 echo "BED:"$design_file
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38 echo "MAN:"$manifest_file
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39 echo "BED chosen:"$BED_PATH
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40 echo "MAN chosen:"$MAN_PATH
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8
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41 echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
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42 echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
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43 echo "VARSCAN_PATH3:"$jar_path
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2
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44
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45 init_file="galaxy_init.sh"
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46 echo '#!/bin/bash' > $init_file
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47
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48 ## executables
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49 #echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file
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50 echo "snpEff=$SNPEFF_JAR_PATH/" >> $init_file
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51 #echo "snpSift=/ccagc/lib/SnpSift" >> $init_file
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52 echo "snpSift=$SNPEFF_JAR_PATH/" >> $init_file
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53 #echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
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54 echo "varscan=$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
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55
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56 ## files
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57 echo "targetBed=$BED_PATH" >> $init_file
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58 echo "manifest=$MAN_PATH" >> $init_file
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59
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60 ## ----------
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61 ## Status / debug
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62 ## ----------
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63 echo "BAM: "$bam_file
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64 echo "OUT: "$bam_name
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65 echo "BAMBASE: "$bam_base
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66 echo "OUTPATH: "$out_path
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67 echo "HTMLOUT: "$html_out
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68 echo "VCFOUT : "$vcf_out
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69 echo "INIT : "$init_file
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7
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70
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5
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71 source $init_file
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7
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72
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5
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73 echo "--- sam ---"
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74 samtools
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75 echo "--- bcf ---"
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76 bcftools
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7
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77 echo "--- snpsift ---"
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78 java -jar $snpSift/SnpSift.jar
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79 echo "--- snpeff ---"
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80 java -jar $snpEff/snpeff.jar
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81 echo "--- varscan ---"
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82 java -jar $varScan
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83
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5
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84 exit 0
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2
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85
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86 ## ----------
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87 ## create output files dir
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88 ## ----------
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89 mkdir $out_path
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90 mkdir $out_path/$bam_base
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91
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92 ## ----------
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93 ## running analysis
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94 ## ----------
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95 echo "Starting VcAn"
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3
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96 $TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base
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2
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97 #$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more
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98
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99 echo "Starting amplicon-Report"
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3
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100 $TOOLDIR/falco/amplicon-Report.sh $bam_base
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2
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101
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102 echo "Starting QC"
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3
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103 $TOOLDIR/falco/amplicon-QC.sh $bam_file
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2
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104
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105 #echo "Starting plots.R"
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106 #$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf
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107
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108 echo "Starting mkHtmlReport"
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3
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109 $TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./
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2
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110
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111
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112
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113 ## ----------
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114 ## create index html for main galaxy output
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115 ## ----------
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116 echo "<!DOCTYPE html>" >> $html_out
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117 echo "<html>" >> $html_out
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118 echo "<head>" >> $html_out
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119 echo "<style>" >> $html_out
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120 echo " body{ padding: 0px 20px; }" >> $html_out
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121 echo " h1{ color: red; }" >> $html_out
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122 echo " table{ border: 1px solid black; padding: 5px }" >> $html_out
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123 echo "</style>" >> $html_out
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124 echo "</head>" >> $html_out
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125 echo "<body>" >> $html_out
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126 echo " <h1>FALCO</h1>" >> $html_out
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127 echo " <a href=\"index.html\">HTML</a>" >> $html_out
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128 echo " <table><tbody>" >> $html_out
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129 #for file in *.vcf *.txt *.tsv
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130 for file in *
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131 do
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132 lineCount=`wc -l $file | cut -f 1 -d " "`
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133 echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
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134 #echo " <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out
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135 done
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136 echo " </tbody></table>" >> $html_out
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137 echo "</body>" >> $html_out
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138 echo "</html>" >> $html_out
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139
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140 ## ----------
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141 ## creating galaxy history outputs
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142 ## ----------
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143 #cp 'index.html' $html_out # this is the overview of samples html
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144 cp $bam_base'.html' $out_path/'out.html' # this is the sample html
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145 cp $bam_base'.vcf' $vcf_out
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146
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147 ## ----------
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148 ## copy files to keep to output path
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149 ## ----------
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150 cp -r ./$bam_base/*png $out_path/$bam_base/
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151 cp -r ./* $out_path
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152 #cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path
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153
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154 ## ----------
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155 echo "END falco sh"
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156 exit 0 |
