Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 46:fee06348bfad draft

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Uploaded
author davidvanzessen
date Wed, 27 Jan 2016 08:39:16 -0500
parents ee7209928db8
children d97e1421aa86
comparison
equal deleted inserted replaced
45:ee7209928db8 46:fee06348bfad
55 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" 55 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
56 USECIRCOS="no" 56 USECIRCOS="no"
57 if [ -d "$CIRCOSDIR" ]; then 57 if [ -d "$CIRCOSDIR" ]; then
58 USECIRCOS="yes" 58 USECIRCOS="yes"
59 fi 59 fi
60 echo "Using Circos: $USECIRCOS"
60 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf 61 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
61 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output 62 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
62 echo " $sample" >> $outputFile 63 echo " $sample" >> $outputFile
63 64
64 if [[ "$USECIRCOS" == "no" ]]; then 65 if [[ "$USECIRCOS" != "yes" ]]; then
65 continue 66 continue
66 fi 67 fi
67 68
68 circos_file="$outputDir/${sample}_VJ_circos.txt" 69 circos_file="$outputDir/${sample}_VJ_circos.txt"
69 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 70 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
70 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 71 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
71 #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
72 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 72 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
73 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png 73 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
74 74
75 75
76 if [[ "$useD" == "true" ]] ; then 76 if [[ "$useD" == "true" ]] ; then
125 done 125 done
126 echo "</div></div>" >> $outputFile 126 echo "</div></div>" >> $outputFile
127 127
128 #circos 128 #circos
129 129
130 if [[ "$USECIRCOS" == "no" ]]; then 130 if [[ "$USECIRCOS" == "yes" ]]; then
131 131
132 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile 132 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
133 for sample in $samples; do 133 for sample in $samples; do
134 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile 134 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
135 if [[ "$useD" == "true" ]] ; then 135 if [[ "$useD" == "true" ]] ; then