Mercurial > repos > davidvanzessen > argalaxy_tools
diff complete.sh @ 58:a073fa12ef98 draft
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| author | davidvanzessen |
|---|---|
| date | Fri, 18 Mar 2016 08:02:22 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/complete.sh Fri Mar 18 08:02:22 2016 -0400 @@ -0,0 +1,67 @@ +#!/bin/bash +set -e +inputFiles=($1) +outputDir=$3 +outputFile=$3/index.html #$1 +clonalType=$4 +species=$5 +locus=$6 +filterproductive=$7 +clonality_method=$8 + +html=$2 +dir="$(cd "$(dirname "$0")" && pwd)" +array=("$@") +echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html +echo "<tr><td>-----------------------------------</td></tr>" >> $html + +#mkdir $PWD/igblastdatabase +#unzip $dir/database.zip -d $PWD/igblastdatabase/ +#export IGDATA=$PWD/igblastdatabase/ + +id="" +forwardSlash="/" +mergerInput=() +echo "Before loop" +count=1 +for current in "${inputFiles[@]}" +do + if [[ "$current" != *"$forwardSlash"* ]]; then + id="$current" + mergerInput+=($id) + count=1 + continue + fi + echo "working on $current" + fileName=$(basename $current) + fileName="${fileName%.*}" + parsedFileName="$PWD/$fileName.parsed" + f=$(file $current) + zipType="Zip archive" + zxType="XZ compressed data" + if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] + then + echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html + fileName=$(basename $current) + bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" + else + echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html + bash ${dir}/igblast/igblast.sh $current $species $locus $parsedFileName + fi + mergerInput+=($parsedFileName) + count=$((count+1)) +done + +echo "<tr><td>-----------------------------------</td></tr>" >> $html +echo "<tr><td>merging</td></tr>" >> $html + +bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt + +echo "<tr><td>done</td></tr>" >> $html +echo "<tr><td>-----------------------------------</td></tr>" >> $html +echo "<tr><td>plotting</td></tr>" >> $html + +echo "after ED" + +bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method +