Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 36:edf2d5882b77 draft

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author davidvanzessen
date Tue, 28 Mar 2017 08:57:05 -0400
parents dc6c53a11d7d
children b6936fb52ab9
comparison
equal deleted inserted replaced
35:dc6c53a11d7d 36:edf2d5882b77
91 circos_file="$outputDir/${sample}_VJ_circos.txt" 91 circos_file="$outputDir/${sample}_VJ_circos.txt"
92 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 92 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
93 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 93 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
94 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 94 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
95 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png 95 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
96 mv $outputDir/circos/circos.pdf $outputDir/circosVJ_${sample}.pdf 96 mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
97 97
98 98
99 if [[ "$useD" == "true" ]] ; then 99 if [[ "$useD" == "true" ]] ; then
100 circos_file="$outputDir/${sample}_VD_circos.txt" 100 circos_file="$outputDir/${sample}_VD_circos.txt"
101 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 101 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
102 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 102 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
103 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 103 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
104 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png 104 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
105 mv $outputDir/circos/circos.pdf $outputDir/circosVD_${sample}.pdf 105 mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
106 106
107 circos_file="$outputDir/${sample}_DJ_circos.txt" 107 circos_file="$outputDir/${sample}_DJ_circos.txt"
108 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 108 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
109 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 109 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
110 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 110 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
111 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png 111 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
112 mv $outputDir/circos/circos.pdf $outputDir/circosDJ_${sample}.pdf 112 mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg
113 fi 113 fi
114 done 114 done
115 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile 115 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
116 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile 116 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile
117 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile 117 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile