Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline
changeset 2:bb8d5c67c129 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 22 Nov 2013 08:12:40 -0500 |
| parents | 9b2567a3ecc9 |
| children | 2b1d3d6843e8 |
| files | combined.sh |
| diffstat | 1 files changed, 10 insertions(+), 7 deletions(-) [+] |
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--- a/combined.sh Wed Nov 20 10:07:25 2013 -0500 +++ b/combined.sh Fri Nov 22 08:12:40 2013 -0500 @@ -1,11 +1,18 @@ #!/bin/bash +export IGDATA=/home/david/Galaxy/galaxy-dist/toolsheddependencies/igBlastn/1.0.0/davidvanzessen/igblast_human/1c64c977624e/ncbi-igblast-1.0.0/; + +clonalType=${@:(-3):1} html=${@:(-2):1} imageDir=${@:(-1):1} dir="$(cd "$(dirname "$0")" && pwd)" -fileCount=`expr $# - 2` +fileCount=`expr $# - 3` array=("$@") echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html +for var in "$@" +do + echo "$var" >> $html +done echo "<tr><td>-----------------------------------</td></tr>" >> $html limit=`expr $fileCount / 2` @@ -57,7 +64,7 @@ outputFile=$html outputDir=$imageDir mkdir $outputDir -Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir 2>&1 +Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 echo "<html>" > $outputFile echo "<img src='VPlot.png'/>" >> $outputFile echo "<img src='DPlot.png'/>" >> $outputFile @@ -79,10 +86,6 @@ count=$((count+1)) done echo "</table>" >> $outputFile +echo "<h1>$clonalType</h1>" >> $outputFile echo "</html>" >> $2 - - -#r_wrapper.sh $in_file $out_file $out_file.files_path - -echo "<tr><td>done</td></tr>" >> $html