# HG changeset patch # User davidvanzessen # Date 1453821004 18000 # Node ID 4c5033eb708fdd69d5d38dbec1e337473fc7ed1e # Parent 4d201d22633dad93e9dd594f018215f70cbfe525 Uploaded diff -r 4d201d22633d -r 4c5033eb708f report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Tue Jan 26 07:59:32 2016 -0500 +++ b/report_clonality/r_wrapper.sh Tue Jan 26 10:10:04 2016 -0500 @@ -31,7 +31,7 @@ cp $dir/script.js $outputDir cp $dir/jquery-1.11.0.min.js $outputDir samples=`cat $outputDir/samples.txt` -#CIRCOSTOOLS="/home/galaxy/Downloads/circos-master/tools" + echo "

Click here for the results

Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)
" > $2 echo "" >> $2 echo "" >> $2 @@ -51,29 +51,31 @@ mkdir $outputDir/circos cp $dir/circos/* $outputDir/circos/ +CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" +CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf for sample in $samples; do #output the samples to a file and create the circos plots with the R script output echo " $sample" >> $outputFile circos_file="$outputDir/${sample}_VJ_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} - cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/ + cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1 - circos -conf $outputDir/circos/circos.conf 2>&1 + $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png if [[ "$useD" == "true" ]] ; then circos_file="$outputDir/${sample}_VD_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} - cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/ - circos -conf $outputDir/circos/circos.conf 2>&1 + cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png circos_file="$outputDir/${sample}_DJ_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} - cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/ - circos -conf $outputDir/circos/circos.conf 2>&1 + cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png fi diff -r 4d201d22633d -r 4c5033eb708f tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 26 07:59:32 2016 -0500 +++ b/tool_dependencies.xml Tue Jan 26 10:10:04 2016 -0500 @@ -28,7 +28,9 @@ +

Sample/Replicate	All	Productive	Unique Productive	Unproductive	Unique Unproductive