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25
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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 source $1
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10
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11 bam_base=`echo $bam_name | sed 's#.bam$##' - `
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12
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13 ## ----------
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14 ## Create extra init script
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15 ## ----------
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16 if [ $design_file != 'None' ] # Galaxy default is "None"
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17 then
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18 BED_PATH=$design_file
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19 else
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20 BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed"
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21 fi
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22
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23 if [ $manifest_file != 'None' ] # Galaxy default is "None"
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24 then
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25 MAN_PATH=$manifest_file
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26 else
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27 MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"
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28 fi
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29
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30 echo "BED:"$design_file
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31 echo "MAN:"$manifest_file
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32 echo "BED chosen:"$BED_PATH
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33 echo "MAN chosen:"$MAN_PATH
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34 #echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
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35 #echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
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36
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37 init_file="galaxy_init.sh"
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38 echo '#!/bin/bash' > $init_file
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39
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40 ## executables
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41 #echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file
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42 #echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file
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43 #echo "snpSift=/ccagc/lib/SnpSift" >> $init_file
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44 #echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
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45 #echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
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46 #echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
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33
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47 echo "samtools=samtools" >> $init_file
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48 echo "bcftools=bcftools" >> $init_file
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25
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49
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50 ## files
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51 echo "targetBed=$BED_PATH" >> $init_file
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52 echo "manifest=$MAN_PATH" >> $init_file
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53
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54 ## ----------
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55 ## Status / debug
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56 ## ----------
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57 echo "BAM: "$bam_file
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58 echo "OUT: "$bam_name
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59 echo "BAMBASE: "$bam_base
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60 #echo "OUTPATH: "$out_path
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61 #echo "HTMLOUT: "$html_out
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62 echo "VCFOUT : "$vcf_out
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63 echo "INIT : "$init_file
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64
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65 source $init_file
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66
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26
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67 echo "------ --- ------"
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68 echo "------ sam ------"
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69 echo "------ --- ------"
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31
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70 $samtools
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26
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71 echo "------ --- ------"
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27
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72 echo "------ bcf ------"
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26
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73 echo "------ --- ------"
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31
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74 $bcftools
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25
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75 #echo "--- snpsift ---"
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76 #java -jar $snpSift/SnpSift.jar
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77 #echo "--- snpeff ---"
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78 #java -jar $snpEff/snpeff.jar
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79 #echo "--- varscan ---"
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80 #java -jar $varScan
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81
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29
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82
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83
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25
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84
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85 ## ----------
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86 ## create output files dir
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87 ## ----------
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26
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88 #mkdir $out_path
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89 #mkdir $out_path/$bam_base
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25
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90
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91 ## ----------
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92 ## running analysis
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93 ## ----------
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94 echo "Starting VcAn"
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29
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95
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96 ## DEBUG
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32
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97 #exit 0
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29
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98
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25
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99 $TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base
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32
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100 echo "...done with VcAn"
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25
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101 #$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more
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102
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103 #echo "Starting amplicon-Report"
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104 #$TOOLDIR/falco/amplicon-Report.sh $bam_base
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105
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106 #echo "Starting QC"
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107 #$TOOLDIR/falco/amplicon-QC.sh $bam_file
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108
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109 #echo "Starting plots.R"
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110 #$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf
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111
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112 #echo "Starting mkHtmlReport"
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113 #$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./
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114
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115
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116
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117 ## ----------
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118 ## create index html for main galaxy output
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119 ## ----------
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120 # echo "<!DOCTYPE html>" >> $html_out
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121 # echo "<html>" >> $html_out
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122 # echo "<head>" >> $html_out
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123 # echo "<style>" >> $html_out
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124 # echo " body{ padding: 0px 20px; }" >> $html_out
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125 # echo " h1{ color: red; }" >> $html_out
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126 # echo " table{ border: 1px solid black; padding: 5px }" >> $html_out
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127 # echo "</style>" >> $html_out
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128 # echo "</head>" >> $html_out
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129 # echo "<body>" >> $html_out
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130 # echo " <h1>FALCO</h1>" >> $html_out
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131 # echo " <a href=\"index.html\">HTML</a>" >> $html_out
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132 # echo " <table><tbody>" >> $html_out
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133 # #for file in *.vcf *.txt *.tsv
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134 # for file in *
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135 # do
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136 # lineCount=`wc -l $file | cut -f 1 -d " "`
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137 # echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
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138 # #echo " <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out
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139 # done
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140 # echo " </tbody></table>" >> $html_out
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141 # echo "</body>" >> $html_out
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142 # echo "</html>" >> $html_out
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143
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144 ## ----------
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145 ## creating galaxy history outputs
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146 ## ----------
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147 #cp 'index.html' $html_out # this is the overview of samples html
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148 #cp $bam_base'.html' $out_path/'out.html' # this is the sample html
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149 cp $bam_base'.vcf' $vcf_out
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150
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151 ## ----------
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152 ## copy files to keep to output path
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153 ## ----------
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154 #cp -r ./$bam_base/*png $out_path/$bam_base/
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155 #cp -r ./* $out_path
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156 #cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path
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157
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158 ## ----------
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159 echo "END falco sh"
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160 exit 0 |
