Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 40:a2fdcf1a2e50 draft

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author davidvanzessen
date Tue, 26 Jan 2016 02:58:17 -0500
parents d7580295e13b
children 85566b336a72
comparison
equal deleted inserted replaced
39:2e0a7c35082e 40:a2fdcf1a2e50
56 echo " $sample" >> $outputFile 56 echo " $sample" >> $outputFile
57 57
58 circos_file="$outputDir/${sample}_VJ_circos.txt" 58 circos_file="$outputDir/${sample}_VJ_circos.txt"
59 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 59 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
60 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ 60 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
61 /home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1 61 #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
62 circos -conf $outputDir/circos/circos.conf 2>&1
62 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png 63 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
63 64
64 65
65 if [[ "$useD" == "true" ]] ; then 66 if [[ "$useD" == "true" ]] ; then
66 circos_file="$outputDir/${sample}_VD_circos.txt" 67 circos_file="$outputDir/${sample}_VD_circos.txt"