Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 45:ee7209928db8 draft

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Uploaded
author davidvanzessen
date Wed, 27 Jan 2016 05:35:55 -0500
parents 4c5033eb708f
children fee06348bfad
comparison
equal deleted inserted replaced
44:4c5033eb708f 45:ee7209928db8
51 51
52 mkdir $outputDir/circos 52 mkdir $outputDir/circos
53 cp $dir/circos/* $outputDir/circos/ 53 cp $dir/circos/* $outputDir/circos/
54 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" 54 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
55 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" 55 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
56 USECIRCOS="no"
57 if [ -d "$CIRCOSDIR" ]; then
58 USECIRCOS="yes"
59 fi
56 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf 60 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
57 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output 61 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
58 echo " $sample" >> $outputFile 62 echo " $sample" >> $outputFile
63
64 if [[ "$USECIRCOS" == "no" ]]; then
65 continue
66 fi
59 67
60 circos_file="$outputDir/${sample}_VJ_circos.txt" 68 circos_file="$outputDir/${sample}_VJ_circos.txt"
61 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 69 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
62 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 70 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
63 #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1 71 #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
117 done 125 done
118 echo "</div></div>" >> $outputFile 126 echo "</div></div>" >> $outputFile
119 127
120 #circos 128 #circos
121 129
122 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile 130 if [[ "$USECIRCOS" == "no" ]]; then
123 for sample in $samples; do 131
124 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile 132 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
125 if [[ "$useD" == "true" ]] ; then 133 for sample in $samples; do
126 echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile 134 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
127 fi 135 if [[ "$useD" == "true" ]] ; then
128 echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile 136 echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
129 if [[ "$useD" == "true" ]] ; then 137 fi
130 echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile 138 echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
131 fi 139 if [[ "$useD" == "true" ]] ; then
132 echo "<center></table></div>" >> $outputFile 140 echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
133 count=$((count+1)) 141 fi
134 done 142 echo "<center></table></div>" >> $outputFile
135 echo "</div></div>" >> $outputFile 143 count=$((count+1))
136 144 done
145 echo "</div></div>" >> $outputFile
146 fi
137 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile 147 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
138 148
139 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" 149 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
140 echo "$hasReplicateColumn" 150 echo "$hasReplicateColumn"
141 #if its a 'new' merged file with replicate info 151 #if its a 'new' merged file with replicate info