Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 45:942eea8359fe draft

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Uploaded
author davidvanzessen
date Fri, 08 Dec 2017 06:32:16 -0500
parents 1d8728f3ff37
children efe0a2b5d163
comparison
equal deleted inserted replaced
44:1d8728f3ff37 45:942eea8359fe
97 if [[ "$USECIRCOS" != "yes" ]]; then 97 if [[ "$USECIRCOS" != "yes" ]]; then
98 continue 98 continue
99 fi 99 fi
100 100
101 circos_file="$outputDir/${sample}_VJ_circos.txt" 101 circos_file="$outputDir/${sample}_VJ_circos.txt"
102 sed -i -- 's%/%:%g' $circos_file
102 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 103 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
103 echo "Circos tools command:" 104 echo "Circos tools command:"
104 echo "cat \"${circos_file}\" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/" 105 echo "cat \"${circos_file}\" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/"
105 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 106 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
106 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt 107
107 echo "Circos command:" 108 echo "Circos command:"
108 echo "$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1" 109 echo "$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1"
109 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 110 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
110 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png 111 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
111 mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg 112 mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
112 113
113 114
114 if [[ "$useD" == "true" ]] ; then 115 if [[ "$useD" == "true" ]] ; then
115 circos_file="$outputDir/${sample}_VD_circos.txt" 116 circos_file="$outputDir/${sample}_VD_circos.txt"
117 sed -i -- 's%/%:%g' $circos_file
116 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 118 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
117 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 119 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
118 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt 120 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
119 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 121 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
120 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png 122 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
121 mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg 123 mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
122 124
123 circos_file="$outputDir/${sample}_DJ_circos.txt" 125 circos_file="$outputDir/${sample}_DJ_circos.txt"
126 sed -i -- 's%/%:%g' $circos_file
124 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 127 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
125 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 128 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
126 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt 129 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
127 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 130 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
128 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png 131 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png