Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 44:4c5033eb708f draft

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Uploaded
author davidvanzessen
date Tue, 26 Jan 2016 10:10:04 -0500
parents 65134a538c5a
children ee7209928db8
comparison
equal deleted inserted replaced
43:4d201d22633d 44:4c5033eb708f
29 cp $dir/tabber.js $outputDir 29 cp $dir/tabber.js $outputDir
30 cp $dir/style.css $outputDir 30 cp $dir/style.css $outputDir
31 cp $dir/script.js $outputDir 31 cp $dir/script.js $outputDir
32 cp $dir/jquery-1.11.0.min.js $outputDir 32 cp $dir/jquery-1.11.0.min.js $outputDir
33 samples=`cat $outputDir/samples.txt` 33 samples=`cat $outputDir/samples.txt`
34 #CIRCOSTOOLS="/home/galaxy/Downloads/circos-master/tools" 34
35 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2 35 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2
36 echo "<table border = 1>" >> $2 36 echo "<table border = 1>" >> $2
37 echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2 37 echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
38 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un 38 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
39 do 39 do
49 echo "productive_counting.txt" 49 echo "productive_counting.txt"
50 echo "<html><head><title>Report on:" >> $outputFile 50 echo "<html><head><title>Report on:" >> $outputFile
51 51
52 mkdir $outputDir/circos 52 mkdir $outputDir/circos
53 cp $dir/circos/* $outputDir/circos/ 53 cp $dir/circos/* $outputDir/circos/
54 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
55 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
54 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf 56 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
55 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output 57 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
56 echo " $sample" >> $outputFile 58 echo " $sample" >> $outputFile
57 59
58 circos_file="$outputDir/${sample}_VJ_circos.txt" 60 circos_file="$outputDir/${sample}_VJ_circos.txt"
59 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 61 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
60 cat "${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 $outputDir/circos/ 62 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
61 #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1 63 #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
62 circos -conf $outputDir/circos/circos.conf 2>&1 64 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
63 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png 65 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
64 66
65 67
66 if [[ "$useD" == "true" ]] ; then 68 if [[ "$useD" == "true" ]] ; then
67 circos_file="$outputDir/${sample}_VD_circos.txt" 69 circos_file="$outputDir/${sample}_VD_circos.txt"
68 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 70 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
69 cat "${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 $outputDir/circos/ 71 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
70 circos -conf $outputDir/circos/circos.conf 2>&1 72 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
71 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png 73 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
72 74
73 circos_file="$outputDir/${sample}_DJ_circos.txt" 75 circos_file="$outputDir/${sample}_DJ_circos.txt"
74 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 76 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
75 cat "${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 $outputDir/circos/ 77 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
76 circos -conf $outputDir/circos/circos.conf 2>&1 78 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
77 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png 79 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
78 80
79 fi 81 fi
80 done 82 done
81 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile 83 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile