Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 71:55d06821d6a5 draft

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author davidvanzessen
date Wed, 17 Aug 2016 08:27:47 -0400
parents 6fdafffd7f0f
children 93c7d58a292c
comparison
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70:6fdafffd7f0f 71:55d06821d6a5
29 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1 29 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
30 cp $dir/tabber.js $outputDir 30 cp $dir/tabber.js $outputDir
31 cp $dir/style.css $outputDir 31 cp $dir/style.css $outputDir
32 cp $dir/script.js $outputDir 32 cp $dir/script.js $outputDir
33 cp $dir/jquery-1.11.0.min.js $outputDir 33 cp $dir/jquery-1.11.0.min.js $outputDir
34 cp $dir/pure-min.css $outputDir
34 samples=`cat $outputDir/samples.txt` 35 samples=`cat $outputDir/samples.txt`
35 36
36 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 37 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
37 echo "<table border = 1>" >> $2 38 echo "<table border = 1>" >> $2
38 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 39 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
87 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png 88 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
88 89
89 fi 90 fi
90 done 91 done
91 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile 92 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
92 echo "<link rel='stylesheet' href='http://yui.yahooapis.com/pure/0.6.0/pure-min.css'>" >> $outputFile 93 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile
93 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile 94 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
94 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile 95 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
95 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile 96 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
96 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile 97 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
97 98