# HG changeset patch # User davidvanzessen # Date 1385125960 18000 # Node ID bb8d5c67c1294de5e6952c22fc05599fd071d78e # Parent 9b2567a3ecc9c8600d9680430b47d67b53c1ddb9 Uploaded diff -r 9b2567a3ecc9 -r bb8d5c67c129 combined.sh --- 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 "

Progress

" > $html +for var in "$@" +do + echo "$var" >> $html +done echo "" >> $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 "" > $outputFile echo "" >> $outputFile echo "" >> $outputFile @@ -79,10 +86,6 @@ count=$((count+1)) done echo "
info
-----------------------------------
" >> $outputFile +echo "

$clonalType

" >> $outputFile echo "" >> $2 - - -#r_wrapper.sh $in_file $out_file $out_file.files_path - -echo "done" >> $html